[1] "ofn"       "-oTLGG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/22506744/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/22533658/transformed.cor.cli.txt"

nPatients in clinical file=515, in cluster file=513, common to both=512
[1]  49 512
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         42                         470 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         42                         470 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           43                           469 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           43                           469 
[1] "AMP PEAK  3(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           24                           488 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           24                           488 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            21                            491 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            21                            491 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         30                         482 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         30                         482 
[1] "AMP PEAK  6(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          127                           385 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          127                           385 
[1] "AMP PEAK  7(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          173                           339 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          173                           339 
[1] "AMP PEAK  8(7Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          181                           331 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          181                           331 
[1] "AMP PEAK  9(8Q24.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            99                            413 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            99                            413 
[1] "AMP PEAK 10(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           46                           466 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           46                           466 
[1] "AMP PEAK 11(10P15.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            71                            441 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            71                            441 
[1] "AMP PEAK 12(11Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            87                            425 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            87                            425 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             72                             440 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             72                             440 
[1] "AMP PEAK 14(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            37                            475 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            37                            475 
[1] "AMP PEAK 15(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          22                          490 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          22                          490 
[1] "AMP PEAK 16(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            19                            493 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            19                            493 
[1] "AMP PEAK 17(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            43                            469 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            43                            469 
[1] "AMP PEAK 18(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           129                            383 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           129                            383 
[1] "AMP PEAK 19(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                            48                            464 
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                            48                            464 
[1] "AMP PEAK 20(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            63                            449 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            63                            449 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           206                            306 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           206                            306 
[1] "DEL PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          196                           316 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          196                           316 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         35                         477 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         35                         477 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           77                           435 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           77                           435 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            49                            463 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            49                            463 
[1] "DEL PEAK  6(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            39                            473 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            39                            473 
[1] "DEL PEAK  7(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         47                         465 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         47                         465 
[1] "DEL PEAK  8(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          137                           375 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          137                           375 
[1] "DEL PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            50                            462 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            50                            462 
[1] "DEL PEAK 10(5Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         64                         448 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         64                         448 
[1] "DEL PEAK 11(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           50                           462 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           50                           462 
[1] "DEL PEAK 12(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            77                            435 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            77                            435 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         81                         431 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         81                         431 
[1] "DEL PEAK 14(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           23                           489 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           23                           489 
[1] "DEL PEAK 15(8Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           29                           483 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           29                           483 
[1] "DEL PEAK 16(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        149                         363 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        149                         363 
[1] "DEL PEAK 17(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          175                           337 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          175                           337 
[1] "DEL PEAK 18(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           151                            361 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           151                            361 
[1] "DEL PEAK 19(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                           104                            408 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                           104                            408 
[1] "DEL PEAK 20(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            72                            440 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            72                            440 
[1] "DEL PEAK 21(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            38                            474 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            38                            474 
[1] "DEL PEAK 22(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          72                          440 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          72                          440 
[1] "DEL PEAK 23(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           144                            368 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           144                            368 
[1] "DEL PEAK 24(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                         110                          402 
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                         110                          402 
[1] "DEL PEAK 25(14Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                           122                            390 
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                           122                            390 
[1] "DEL PEAK 26(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          78                          434 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          78                          434 
[1] "DEL PEAK 27(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            278                             234 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            278                             234 
[1] "DEL PEAK 28(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             77                             435 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             77                             435 
[1] "DEL PEAK 29(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           78                           434 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           78                           434 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "DAYS_TO_LAST_KNOWN_ALIVE"            
 [9] "RADIATION_THERAPY"                   
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "HISTOLOGICAL_TYPE"                   
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 512 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=120,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=331,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 512 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1Q22) MUTATED    26  16
  AMP PEAK  1(1Q22) WILD-TYPE 357 109
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         42                         466 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         16                         109 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-CS-6665 TCGA-CS-4941 TCGA-DB-A64L TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-6396 
       51.55         7.69        24.20        30.21       211.17        75.16 
TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7304 
        1.22        11.64        14.99        90.77        10.36        23.31 
TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A6S7 TCGA-DU-A7TB 
       14.60        19.13        31.69        24.43        20.98        51.52 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-FG-5962 
       50.14        41.13        95.57        14.30        51.88        47.77 
TCGA-FG-8185 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-8108 
       14.24        17.42        24.26        16.24        31.69         2.50 
TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-HW-A5KM TCGA-QH-A6CV TCGA-S9-A6WM TCGA-S9-A7R1 
        0.23        20.22        20.71        14.53        19.86       169.84 
TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CA TCGA-VM-A8CF TCGA-WH-A86K 
       24.92        28.08        24.16        13.51        20.02        13.32 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 
       45.60        42.77        59.38       117.50        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        63.88        46.06 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       24.59        27.81        17.19        17.19        54.25        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       65.75        87.45         7.04       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       154.36       105.21         6.54         8.84       117.40 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       30.67        26.30         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        41.98         2.76         5.10        23.74 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        33.27 
TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       29.85        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
       95.11        22.29        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
      139.04        84.33        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        0.56        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       16.18        21.30        75.02        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       39.48         0.23         0.20        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       18.38        18.71        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 
        0.13         0.03        16.54         3.75         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
       14.27         0.16         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       33.01        12.23         6.25         0.10         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       28.87        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        7.99         2.37         2.30         9.44         5.88         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.59         1.28         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       27.16        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       65.39        16.18        59.05        40.64        30.44        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        45.93        43.20 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        39.16        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21         8.05        51.06        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       0.23                        0.03 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     211.17                      182.33 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     22.145                      22.355 
[1] "0.2 - 211.2 (22.1)" "0.0 - 182.3 (22.4)"
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    19  23
  AMP PEAK  1(1Q22) WILD-TYPE 209 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     19   23
  AMP PEAK  1(1Q22) WILD-TYPE  209  261
        clus
vv       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  FEMALE                        19                         209
  MALE                          23                         261
[1] 2 2
[1] FALSE
D1V4, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    12  29
  AMP PEAK  1(1Q22) WILD-TYPE 172 266
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     12   29
  AMP PEAK  1(1Q22) WILD-TYPE  172  266
     clus
vv    AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  NO                         12                         172
  YES                        29                         266
[1] 2 2
[1] FALSE
D1V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  1(1Q22) MUTATED            19                6                17
  AMP PEAK  1(1Q22) WILD-TYPE         175              123               172
D1V6, multiclass
                   clus
vv                  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  ASTROCYTOMA                              19                         175
  OLIGOASTROCYTOMA                          6                         123
  OLIGODENDROGLIOMA                        17                         172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q22) MUTATED                                  0     2
  AMP PEAK  1(1Q22) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED                           2    37
  AMP PEAK  1(1Q22) WILD-TYPE                        19   435
D1V7, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   37
                                  clus
vv                                 AMP PEAK  1(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED     0  39
  AMP PEAK  1(1Q22) WILD-TYPE  32 407
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      0   39
  AMP PEAK  1(1Q22) WILD-TYPE   32  407
                        clus
vv                       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             0                          32
  NOT HISPANIC OR LATINO                        39                         407
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q32.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q32.1) MUTATED    22  21
  AMP PEAK  2(1Q32.1) WILD-TYPE 361 104
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           43                           465 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           21                           104 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-CS-6665 TCGA-E1-A7YN TCGA-CS-4941 TCGA-CS-5395 TCGA-DB-5277 TCGA-DB-A64L 
       51.55        23.90         7.69        21.01        50.86        24.20 
TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 
       30.21       211.17         1.22        11.64        14.99        90.77 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7304 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT 
       10.36         7.96        23.31        14.60        19.13        24.43 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-E1-A7YD TCGA-E1-A7YQ TCGA-FG-5962 TCGA-FG-6688 
       51.52         7.50        14.30        51.88        47.77        18.77 
TCGA-FG-A4MW TCGA-HT-7475 TCGA-HT-7603 TCGA-HT-7688 TCGA-HT-8011 TCGA-HT-8104 
       18.38        17.42        23.18        31.69        16.24        12.23 
TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-QH-A6CV TCGA-QH-A6CX TCGA-S9-A6WM TCGA-S9-A7R1 
        0.23        20.22        14.53        12.23        19.86       169.84 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I TCGA-VM-A8CA TCGA-VM-A8CF 
       10.39        54.77        24.92        28.08        13.51        20.02 
TCGA-WH-A86K 
       13.32 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 
       20.09        17.82        20.45        18.64        21.40        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       42.77        59.38       117.50        43.89        36.36        60.10 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.26        53.62         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       37.38        46.95        48.30        49.94        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        91.13        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       36.56        78.28        46.42        18.84        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P 
       37.45        33.57        72.95        31.63        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F 
       19.96        63.88        46.06        24.59        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        23.21        17.46        13.71        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         2.40        11.47        62.96       156.23       154.36 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        30.67        26.30 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       94.32        18.94        44.02        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10        23.74        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        33.27        29.85        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       22.29        11.41        26.76        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       84.33        37.38        44.42        38.89         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
       12.43        16.18        21.30        75.02        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       36.82        14.93        42.54        41.33        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       10.72        18.71        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43         1.64         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       28.87        20.71        19.00        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.96         7.59         1.28         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       27.16        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       20.48        48.33        49.32        34.78        65.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        30.44        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
       61.41        26.99        31.36        45.93        43.20         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        39.16        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.23                          0.03 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        19.86                         23.21 
[1] "0.2 - 211.2 (19.9)" "0.0 - 182.3 (23.2)"
[1] "hr=" "2.2"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    19  24
  AMP PEAK  2(1Q32.1) WILD-TYPE 209 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     19   24
  AMP PEAK  2(1Q32.1) WILD-TYPE  209  260
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          19                           209
  MALE                            24                           260
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    10  31
  AMP PEAK  2(1Q32.1) WILD-TYPE 174 264
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     10   31
  AMP PEAK  2(1Q32.1) WILD-TYPE  174  264
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           10                           174
  YES                          31                           264
[1] 2 2
[1] FALSE
D2V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  2(1Q32.1) MUTATED            22                7                14
  AMP PEAK  2(1Q32.1) WILD-TYPE         172              122               175
D2V6, multiclass
                   clus
vv                  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  ASTROCYTOMA                                22                           172
  OLIGOASTROCYTOMA                            7                           122
  OLIGODENDROGLIOMA                          14                           175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q32.1) MUTATED                                  0     2
  AMP PEAK  2(1Q32.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED                           3    37
  AMP PEAK  2(1Q32.1) WILD-TYPE                        18   435
D2V7, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     37
                                  clus
vv                                 AMP PEAK  2(1Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      435
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED     0  40
  AMP PEAK  2(1Q32.1) WILD-TYPE  32 406
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      0   40
  AMP PEAK  2(1Q32.1) WILD-TYPE   32  406
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                32
  NOT HISPANIC OR LATINO                           406
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2P24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.3) MUTATED    14  10
  AMP PEAK  3(2P24.3) WILD-TYPE 369 115
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           24                           484 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           10                           115 
$`AMP PEAK  3(2P24.3) MUTATED`
TCGA-DB-5274 TCGA-DB-5277 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-6407 TCGA-DU-8165 
       75.25        50.86        30.21        54.25        94.52        19.13 
TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YV TCGA-FG-A711 TCGA-HT-8564 TCGA-HT-A4DS 
       41.13        14.30        32.45        48.69        15.72         0.23 
TCGA-HT-A5R5 TCGA-HT-A61B TCGA-HW-A5KM TCGA-P5-A5F2 TCGA-S9-A6U0 TCGA-S9-A6WM 
        0.13        17.52        20.71         7.96        24.39        19.86 
TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-TQ-A7RK TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VW-A8FI 
       20.02        25.38        44.09        13.51         7.89         8.05 

$`AMP PEAK  3(2P24.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       43.89        36.36        60.10        40.18         0.26        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 
       53.62         6.38        17.69        26.76        37.38        46.95 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
       48.30        49.94        49.12       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US 
       46.06        24.59        27.81        17.19        17.19        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        16.83       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        2.40        11.47        62.96       156.23       154.36        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       22.29        11.41        26.76        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        12.43        16.18        21.30        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       20.09        28.34        13.68        14.24        16.01        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       23.70        14.76        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       28.54        10.78        36.66         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       28.27        26.04        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       28.87        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 
        7.99         2.37         2.30         9.44         5.88         7.59 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 
       18.77        41.10        40.93        35.38        36.82        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        26.93        23.51        19.99         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       20.48        54.77        48.33        49.32        34.78        65.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       24.92        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       36.69        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        45.93        43.20 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                        94.52                        211.17 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       20.365                        22.470 
[1] "0.1 - 94.5 (20.4)"  "0.0 - 211.2 (22.5)"
[1] "hr=" "2.1"
D3V2, continuous
D3V3, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED    11  13
  AMP PEAK  3(2P24.3) WILD-TYPE 217 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     11   13
  AMP PEAK  3(2P24.3) WILD-TYPE  217  271
        clus
vv       AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  FEMALE                          11                           217
  MALE                            13                           271
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     7  15
  AMP PEAK  3(2P24.3) WILD-TYPE 177 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      7   15
  AMP PEAK  3(2P24.3) WILD-TYPE  177  280
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NO                            7                           177
  YES                          15                           280
[1] 2 2
[1] FALSE
D3V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  3(2P24.3) MUTATED            13                3                 8
  AMP PEAK  3(2P24.3) WILD-TYPE         181              126               181
D3V6, multiclass
                   clus
vv                  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ASTROCYTOMA                                13                           181
  OLIGOASTROCYTOMA                            3                           126
  OLIGODENDROGLIOMA                           8                           181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(2P24.3) MUTATED                                  0     0
  AMP PEAK  3(2P24.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2P24.3) MUTATED                           0    23
  AMP PEAK  3(2P24.3) WILD-TYPE                        21   449
D3V7, multiclass
                                  clus
vv                                 AMP PEAK  3(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     23
                                  clus
vv                                 AMP PEAK  3(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      449
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     3  18
  AMP PEAK  3(2P24.3) WILD-TYPE  29 428
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      3   18
  AMP PEAK  3(2P24.3) WILD-TYPE   29  428
                        clus
vv                       AMP PEAK  3(2P24.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK  3(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                29
  NOT HISPANIC OR LATINO                           428
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(3Q26.33) MUTATED    10  10
  AMP PEAK  4(3Q26.33) WILD-TYPE 373 115
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            20                            488 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            10                            115 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-CS-4942 TCGA-CS-5395 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-DU-A5TW 
       43.89        21.01         1.22         8.84         5.10        24.99 
TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YL TCGA-FG-5962 TCGA-FG-7636 TCGA-FG-A6J3 
       41.13        14.30        16.18        47.77        17.88        22.26 
TCGA-HT-7606 TCGA-HT-7676 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-QH-A870 TCGA-S9-A6WM 
       17.29         0.16         0.23        27.35        12.99        19.86 
TCGA-TM-A84B TCGA-VW-A8FI 
       24.92         8.05 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 
       36.36        60.10        40.18         0.26        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       46.06        24.59        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        23.21        17.46        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         2.40        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 
      154.36        14.99       105.21         6.54       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       26.17        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       22.29        11.41        26.76        21.30        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57       130.78        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       19.46        12.43        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
      145.05        32.35        39.48         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        15.35        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       48.69         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27        15.72        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        16.83        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        56.58        45.44 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       41.49        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       42.54        24.92        31.63        12.76        28.87        20.71 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        14.40        14.40         0.23         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         9.44         5.88         7.96         7.59 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       16.73         1.91        16.50        16.70        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       94.03        32.65        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        40.93        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       65.39        16.18        59.05        40.64        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       14.93        23.80        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       45.93        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       20.02        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                         47.77                         211.17 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                        17.585                         23.195 
[1] "0.2 - 47.8 (17.6)"  "0.0 - 211.2 (23.2)"
[1] "hr=" "4.4"
D4V2, continuous
D4V3, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED    10  11
  AMP PEAK  4(3Q26.33) WILD-TYPE 218 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED     10   11
  AMP PEAK  4(3Q26.33) WILD-TYPE  218  273
        clus
vv       AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  FEMALE                           10                            218
  MALE                             11                            273
[1] 2 2
[1] FALSE
D4V4, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     5  13
  AMP PEAK  4(3Q26.33) WILD-TYPE 179 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      5   13
  AMP PEAK  4(3Q26.33) WILD-TYPE  179  282
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                             5                            179
  YES                           13                            282
[1] 2 2
[1] FALSE
D4V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  4(3Q26.33) MUTATED            16                1                 4
  AMP PEAK  4(3Q26.33) WILD-TYPE         178              128               185
D4V6, multiclass
                   clus
vv                  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  ASTROCYTOMA                                 16                            178
  OLIGOASTROCYTOMA                             1                            128
  OLIGODENDROGLIOMA                            4                            185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(3Q26.33) MUTATED                                  0     0
  AMP PEAK  4(3Q26.33) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED                           3    18
  AMP PEAK  4(3Q26.33) WILD-TYPE                        18   454
D4V7, multiclass
                                  clus
vv                                 AMP PEAK  4(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      18
                                  clus
vv                                 AMP PEAK  4(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       454
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     0  19
  AMP PEAK  4(3Q26.33) WILD-TYPE  32 427
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      0   19
  AMP PEAK  4(3Q26.33) WILD-TYPE   32  427
                        clus
vv                       AMP PEAK  4(3Q26.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       AMP PEAK  4(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            427
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    17  13
  AMP PEAK  5(4Q12) WILD-TYPE 366 112
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         30                         478 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         13                         112 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-CS-6665 TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A75O TCGA-DH-A7UU 
       51.55        36.36        46.95        50.86        30.74        13.71 
TCGA-DU-7010 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A7TD 
       14.99        60.30         2.76        31.69        24.43         7.50 
TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YI TCGA-E1-A7YL TCGA-FG-A6J3 
       41.13        57.93        14.30         3.65        16.18        22.26 
TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-7856 TCGA-HT-7882 TCGA-HT-A5R7 TCGA-S9-A6U0 
        5.72        24.26        39.09         3.72        20.22        24.39 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A84I TCGA-VW-A8FI 
       14.07         7.92        20.02        20.48        28.08         8.05 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        26.76        37.38        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        91.13 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       16.18        19.96        63.88        46.06        24.59        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       154.36       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 
        7.96        94.32        18.94        44.02        25.91        23.31 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        33.27        29.85 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
       20.98        22.29        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI 
      139.04        84.33        51.52        37.38        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
        0.56        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YK 
       95.57       130.78        29.13        93.21        19.46        12.43 
TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       21.30        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
       48.69        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       28.27        15.72         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       24.92        31.63        12.76        28.87        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         9.44         5.88         7.96         7.59         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       13.41         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50        16.70        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       94.03        32.65        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       41.10        40.93        35.38        36.82        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX 
       19.86        26.47        18.61        18.64        36.13        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        19.99         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        45.93        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       2.76                        0.03 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      60.30                      211.17 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      21.37                       22.47 
[1] "2.8 - 60.3 (21.4)"  "0.0 - 211.2 (22.5)"
[1] "hr=" "2.7"
D5V2, continuous
D5V3, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    12  18
  AMP PEAK  5(4Q12) WILD-TYPE 216 266
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     12   18
  AMP PEAK  5(4Q12) WILD-TYPE  216  266
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        12                         216
  MALE                          18                         266
[1] 2 2
[1] FALSE
D5V4, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     5  24
  AMP PEAK  5(4Q12) WILD-TYPE 179 271
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      5   24
  AMP PEAK  5(4Q12) WILD-TYPE  179  271
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          5                         179
  YES                        24                         271
[1] 2 2
[1] FALSE
D5V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  5(4Q12) MUTATED            21                2                 7
  AMP PEAK  5(4Q12) WILD-TYPE         173              127               182
D5V6, multiclass
                   clus
vv                  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  ASTROCYTOMA                              21                         173
  OLIGOASTROCYTOMA                          2                         127
  OLIGODENDROGLIOMA                         7                         182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(4Q12) MUTATED                                  0     0
  AMP PEAK  5(4Q12) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED                           1    29
  AMP PEAK  5(4Q12) WILD-TYPE                        20   443
D5V7, multiclass
                                  clus
vv                                 AMP PEAK  5(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   29
                                  clus
vv                                 AMP PEAK  5(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    443
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     1  28
  AMP PEAK  5(4Q12) WILD-TYPE  31 418
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      1   28
  AMP PEAK  5(4Q12) WILD-TYPE   31  418
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          31
  NOT HISPANIC OR LATINO                        28                         418
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P11.2) MUTATED    73  54
  AMP PEAK  6(7P11.2) WILD-TYPE 310  71
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          127                           381 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                           54                            71 
$`AMP PEAK  6(7P11.2) MUTATED`
TCGA-CS-6665 TCGA-CS-6670 TCGA-E1-A7YN TCGA-HT-A619 TCGA-CS-4941 TCGA-CS-4942 
       51.55        46.88        23.90        21.40         7.69        43.89 
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18        21.01        53.62         6.38        17.69        26.76 
TCGA-DB-5270 TCGA-DB-A4X9 TCGA-DB-A4XE TCGA-DB-A64O TCGA-DH-5142 TCGA-DH-A669 
      122.73        46.42        37.45        25.48        63.88        30.21 
TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 
       17.19        17.46        18.61         6.74         8.45       211.17 
TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       49.02         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 
       16.83        94.52         7.96        11.47       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 
        8.84       117.40        90.77         7.96         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       14.60        20.68        19.13        16.96        29.85        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TA 
       26.17        24.99        33.96        11.41        26.76        84.33 
TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YJ 
        7.50         0.56        41.13       130.78        14.30        19.46 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7Z2 TCGA-FG-5962 TCGA-FG-6688 
       16.18        21.30        51.88        13.08        47.77        18.77 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-A4MU 
       41.33        18.44        15.35        20.09        13.68        10.72 
TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7688 
       18.38        10.78         5.72        16.54        24.26        31.69 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 
        0.49         3.72        16.24        63.55        12.23        13.78 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC 
       15.72         0.23         0.13         0.07        27.35         5.33 
TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HW-A5KK 
       16.14        17.65         2.43        10.52        15.35        12.76 
TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A736 TCGA-QH-A6CS 
       14.40         2.30         9.44         0.23         7.56        19.33 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A845 
       14.53        12.23         1.91        16.50        16.70        19.59 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       35.38        24.39        19.86        36.13        26.93        19.99 
TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H 
       20.02        10.39        54.77        34.78        24.92        30.44 
TCGA-TM-A84M TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VW-A8FI 
       24.79        15.98         2.04        36.69        30.05         8.05 
TCGA-WY-A85E 
       20.81 

$`AMP PEAK  6(7P11.2) WILD-TYPE`
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 
       46.72        31.82        42.05        62.01        17.16        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M 
       17.82        20.45        18.64        45.60        42.77        59.38 
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6290 TCGA-CS-6666 
      117.50        36.36        60.10         0.26        37.38        46.95 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       48.30        49.94        49.12        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        91.13        44.52        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       18.84        30.21        39.78        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       24.20        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       30.74        16.18        19.96        46.06        24.59        27.81 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 
       17.19        54.25        23.21        13.71        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        52.11        22.42        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
       87.45       114.08         2.40        62.96       156.23       154.36 
TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 
       14.99        30.67        26.30        10.36        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 
       21.40        15.48        14.17        33.27        31.69        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 
       21.57        95.11        20.98        22.29        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
      139.04        51.52        37.38        44.42        38.89        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS 
       29.13        93.21         3.65        12.43        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        32.45        36.82       146.14        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       36.82        14.93        42.54        17.88        22.55        20.61 
TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       28.34        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       38.27        18.71        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FN-7833 
       16.44        22.26        28.54        36.66        48.69        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 
       35.47        11.28        31.43         1.64         9.40         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        5.56         0.23        29.59        34.19        28.27        26.04 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       20.22         0.10         2.70        16.93         1.81        16.83 
TCGA-HT-A61B TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       17.52        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       24.92        31.63        28.87        20.71        19.00        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         7.99         2.37         5.88         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        7.59         1.28        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
        9.01        13.61         9.60        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.04        14.83        13.61        13.41         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       14.53        16.34        16.73        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       94.03        32.65        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        30.67        62.17        87.12        18.77        41.10 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       40.93        36.82        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.64        14.07         7.92        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       169.84 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        20.48 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       48.33        49.32        65.39        16.18        59.05        40.64 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        24.16        40.83        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       14.93        23.80        21.37        19.69        40.41        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       33.73        31.20        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        45.93        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                        18.61                         24.92 
[1] "0.1 - 211.2 (18.6)" "0.0 - 182.3 (24.9)"
[1] "hr=" "3"  
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    62  65
  AMP PEAK  6(7P11.2) WILD-TYPE 166 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     62   65
  AMP PEAK  6(7P11.2) WILD-TYPE  166  219
        clus
vv       AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  FEMALE                          62                           166
  MALE                            65                           219
[1] 2 2
[1] FALSE
D6V4, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    29  86
  AMP PEAK  6(7P11.2) WILD-TYPE 155 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     29   86
  AMP PEAK  6(7P11.2) WILD-TYPE  155  209
     clus
vv    AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  NO                           29                           155
  YES                          86                           209
[1] 2 2
[1] FALSE
D6V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  6(7P11.2) MUTATED            57               33                37
  AMP PEAK  6(7P11.2) WILD-TYPE         137               96               152
D6V6, multiclass
                   clus
vv                  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  ASTROCYTOMA                                57                           137
  OLIGOASTROCYTOMA                           33                            96
  OLIGODENDROGLIOMA                          37                           152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(7P11.2) MUTATED                                  1     2
  AMP PEAK  6(7P11.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P11.2) MUTATED                          10   114
  AMP PEAK  6(7P11.2) WILD-TYPE                        11   358
D6V7, multiclass
                                  clus
vv                                 AMP PEAK  6(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    114
                                  clus
vv                                 AMP PEAK  6(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED     8 113
  AMP PEAK  6(7P11.2) WILD-TYPE  24 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED      8  113
  AMP PEAK  6(7P11.2) WILD-TYPE   24  333
                        clus
vv                       AMP PEAK  6(7P11.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         113
                        clus
vv                       AMP PEAK  6(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                24
  NOT HISPANIC OR LATINO                           333
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7Q31.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7Q31.2) MUTATED   112  61
  AMP PEAK  7(7Q31.2) WILD-TYPE 271  64
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          173                           335 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                           61                            64 
$`AMP PEAK  7(7Q31.2) MUTATED`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DU-A76O TCGA-E1-A7YN TCGA-HT-A619 TCGA-CS-4938 
       51.55        46.88        17.16        23.90        21.40       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        7.69        43.89        21.01        53.62         6.38        17.69 
TCGA-CS-6188 TCGA-DB-5270 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       26.76       122.73        46.42        30.21        39.78        37.45 
TCGA-DB-A64O TCGA-DB-A64X TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66G 
       25.48        18.51        24.59        30.21        27.81        17.19 
TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 
       17.46        18.61        14.56         8.45         6.81        17.49 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 
      211.17        49.02        65.75         1.22         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 
      133.74        19.89        16.83        94.52         7.96        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8163 
      117.40         7.96        25.91        41.98        23.74        20.68 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       19.13        16.96        29.85        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 
       33.96        95.11        11.41        26.76        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 
       84.33         7.50         0.56        50.14        41.13       130.78 
TCGA-E1-A7YD TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7Z3 TCGA-F6-A8O4 
       14.30        16.18        21.30        51.88        73.48         0.20 
TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       47.77        36.82        18.77        42.54        41.33        18.44 
TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW 
       15.35        20.09        13.68        16.01        10.72        18.38 
TCGA-FG-A60L TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7475 
       21.53        10.78        48.69         5.72        16.54        17.42 
TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-7860 
       24.26       122.47        56.09        31.69        17.52         0.49 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 
        3.72        11.28        16.24        63.55        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 
       13.78        34.19        15.72         0.23         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61C 
        0.07        27.35         5.33         1.81        16.14        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7495 
        2.43        10.52        15.35        11.05         0.10        35.44 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F0 
       24.92        31.63        14.40         0.23         2.30         9.44 
TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A736 TCGA-QH-A6CS 
        5.88         0.23         9.01        13.61         7.56        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       14.83        14.53        12.23        10.29         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
       16.70        12.99        19.59        35.38        24.39        19.86 
TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
       18.61        36.13        26.93        19.99        20.02        15.06 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       28.37       169.84        10.39        54.77        48.33        34.78 
TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TQ-A7RH TCGA-TQ-A7RI 
       24.92        30.44        40.83        24.79        15.98         2.04 
TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VW-A7QS TCGA-VW-A8FI TCGA-WY-A85E 
       36.69        30.05        23.21         8.05        20.81 

$`AMP PEAK  7(7Q31.2) WILD-TYPE`
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K 
       46.72        31.82        42.05        62.01        20.09        17.82 
TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4943 
       20.45        18.64        45.60        42.77        59.38        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
       60.10        40.18         0.26        37.38        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.94        49.12        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA 
       50.86        91.13        44.52        36.56        78.28        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 
       46.06        17.19        54.25        23.21        13.71        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 
       17.46         6.74        13.38       182.33        18.94        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 
       52.11        22.42        75.16        46.06        87.45       114.08 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        2.40        62.96        90.77        30.67        26.30        10.36 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       94.32        18.94        44.02        60.30        23.31         2.76 
TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
        5.10        14.60        21.40        15.48        14.17        33.27 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A7T6 
       31.69        25.55        21.57        20.98        22.29        17.98 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5303 TCGA-E1-5305 
       51.52        37.38        44.42        38.89        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YE TCGA-E1-A7YH 
       57.93       134.27        78.21        95.57        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
        3.65        19.46        12.43        75.02        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       32.45        36.82       146.14        13.08       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 
       39.48         0.23        25.48        52.21        14.93        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8189 
       22.55        20.61        28.34        14.24        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A6IZ 
       32.61        38.27        18.71        23.70        14.76        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 
       16.44        22.26        28.54        36.66        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        6.67        11.54        40.11         0.13         0.03         3.75 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      172.77         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 
       17.29         3.16        22.06        45.99        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 
        5.33        35.47        31.43         1.64         9.40         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01         6.25         0.10         0.46         5.56 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HT-A614 
        0.23        29.59        28.27        26.04         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.93        16.83        17.52        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       68.32        69.27        39.75        40.01        42.54        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX 
       28.87        20.71        19.00        14.40         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X 
        2.37         7.96         7.59         1.28        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       11.64        10.95         9.60        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        13.61        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       16.73        11.08        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS 
        5.46         9.90        28.08         2.07        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 
       87.12        18.77        41.10        40.93        36.82        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY 
       31.10        26.47        18.64        14.07         7.92        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R3 
        8.19         2.04        20.68        18.54        27.16        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 
       30.05        98.63        31.59        18.71        20.48        49.32 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       65.39        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ 
       19.69        40.41        44.09        33.73        31.20        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       23.47        37.05        16.01        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                        19.59                         25.38 
[1] "0.1 - 211.2 (19.6)" "0.0 - 182.3 (25.4)"
[1] "hr=" "2"  
D7V2, continuous
D7V3, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    88  85
  AMP PEAK  7(7Q31.2) WILD-TYPE 140 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     88   85
  AMP PEAK  7(7Q31.2) WILD-TYPE  140  199
        clus
vv       AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  FEMALE                          88                           140
  MALE                            85                           199
[1] 2 2
[1] FALSE
D7V4, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    45 112
  AMP PEAK  7(7Q31.2) WILD-TYPE 139 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     45  112
  AMP PEAK  7(7Q31.2) WILD-TYPE  139  183
     clus
vv    AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  NO                           45                           139
  YES                         112                           183
[1] 2 2
[1] FALSE
D7V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  7(7Q31.2) MUTATED            74               47                52
  AMP PEAK  7(7Q31.2) WILD-TYPE         120               82               137
D7V6, multiclass
                   clus
vv                  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  ASTROCYTOMA                                74                           120
  OLIGOASTROCYTOMA                           47                            82
  OLIGODENDROGLIOMA                          52                           137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(7Q31.2) MUTATED                                  1     4
  AMP PEAK  7(7Q31.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q31.2) MUTATED                          13   155
  AMP PEAK  7(7Q31.2) WILD-TYPE                         8   317
D7V7, multiclass
                                  clus
vv                                 AMP PEAK  7(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    155
                                  clus
vv                                 AMP PEAK  7(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED     9 159
  AMP PEAK  7(7Q31.2) WILD-TYPE  23 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED      9  159
  AMP PEAK  7(7Q31.2) WILD-TYPE   23  287
                        clus
vv                       AMP PEAK  7(7Q31.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       AMP PEAK  7(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                23
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7Q32.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7Q32.3) MUTATED   117  64
  AMP PEAK  8(7Q32.3) WILD-TYPE 266  61
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          181                           327 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                           64                            61 
$`AMP PEAK  8(7Q32.3) MUTATED`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DU-A76O TCGA-E1-A7YN TCGA-HT-A619 TCGA-CS-4938 
       51.55        46.88        17.16        23.90        21.40       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        7.69        43.89        21.01        53.62         6.38        17.69 
TCGA-CS-6188 TCGA-DB-5270 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD 
       26.76       122.73        78.28        46.42        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A64X TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       37.45        25.48        18.51        24.59        30.21        27.81 
TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-5855 
       17.19        17.46        18.61        14.56         8.45         6.81 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 
       17.49       211.17        49.02        65.75         1.22         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       11.47       156.23       154.36        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 
        8.84       117.40        90.77         7.96        25.91        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
        2.76        23.74        14.60        20.68        19.13        16.96 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 
       29.85        24.43        26.17        24.99        33.96        95.11 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TD 
       11.41        26.76        21.30       139.04        84.33         7.50 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD 
       38.89         0.56        50.14        41.13       130.78        14.30 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 
       16.18        21.30        51.88        13.08        73.48        32.35 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
        0.20        47.77        36.82        18.77        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU 
       18.44        15.35        20.09        13.68        16.01        10.72 
TCGA-FG-A4MW TCGA-FG-A60L TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7473 
       18.38        21.53        10.78        48.69         5.72        16.54 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7692 
       17.42        24.26       122.47        56.09        31.69         2.96 
TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 
       17.52         0.49         3.72        11.28        16.24        63.55 
TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS 
       12.23         2.50        13.78        34.19        15.72         0.23 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 
        0.13         0.07        27.35         5.33         1.81        16.14 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EV 
       35.44        24.92        31.63        20.71        14.40         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A731 TCGA-P5-A733 
        2.30         9.44         5.88         0.23         9.01        13.61 
TCGA-P5-A736 TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 
        7.56        19.33        14.83        14.53        12.23        10.29 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TY 
        1.91        16.50        16.70        12.99        19.59        35.38 
TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       24.39        19.86        18.61        36.13        26.93        19.99 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 
       20.02        15.06        18.54        28.37       169.84        10.39 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       54.77        48.33        34.78        24.92        30.44        24.79 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-VW-A7QS TCGA-VW-A8FI 
       15.98         2.04        36.69        30.05        23.21         8.05 
TCGA-WY-A85E 
       20.81 

$`AMP PEAK  8(7Q32.3) WILD-TYPE`
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K 
       46.72        31.82        42.05        62.01        20.09        17.82 
TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4943 
       20.45        18.64        45.60        42.77        59.38        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
       60.10        40.18         0.26        37.38        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.94        49.12        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4XA TCGA-DB-A4XF 
       50.86        91.13        44.52        36.56        18.84        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        24.20        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        63.88        46.06 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5851 
       17.19        54.25        23.21        13.71        18.02        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6393 
        6.74        13.38       182.33        18.94        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 
       22.42        75.16        46.06        87.45       114.08         2.40 
TCGA-DU-7007 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 
       62.96        30.67        26.30        10.36        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8167 
       44.02        60.30        23.31         5.10        21.40        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 
       14.17        33.27        31.69        25.55        21.57        20.98 
TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5303 
       22.29        17.98        51.52        37.38        44.42        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YE 
       79.99        57.93       134.27        78.21        95.57        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS 
       93.21         3.65        19.46        12.43        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z4 TCGA-EZ-7264 
        0.76        32.45        36.82       146.14       145.05        39.48 
TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 
        0.23        25.48        52.21        14.93        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       20.61        28.34        14.24        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       38.27        18.71        23.70        14.76        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       22.26        28.54        36.66        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 
       11.54        40.11         0.13         0.03         3.75         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 
        0.10        14.96         0.10         0.10         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.10         0.46         5.56         0.23        29.59 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       28.27        26.04        20.22         0.10         2.70        16.93 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       16.83        17.52        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       69.27        39.75        40.01        42.54        12.76        28.87 
TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F2 
       19.00        14.40         6.71         7.99         2.37         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        7.59         1.28        10.42        13.25        11.64        10.95 
TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        9.60        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CW 
       15.16         2.53        12.62        15.85        14.04        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X 
       13.41         9.17        14.53        16.34        16.73        11.08 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       41.10        40.93        36.82        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
      135.22        85.55        38.56        84.99        31.10        26.47 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.64        14.07         7.92        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       20.68        27.16        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       18.71        20.48        49.32        65.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        28.08        24.16        40.83        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RJ 
       18.61        14.93        23.80        21.37        19.69        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       44.09        33.73        31.20        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       61.41        26.99        31.36        45.93        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        23.47        37.05 
TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       16.01        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                        19.33                         25.48 
[1] "0.1 - 211.2 (19.3)" "0.0 - 182.3 (25.5)"
[1] "hr=" "2"  
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    93  88
  AMP PEAK  8(7Q32.3) WILD-TYPE 135 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     93   88
  AMP PEAK  8(7Q32.3) WILD-TYPE  135  196
        clus
vv       AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  FEMALE                          93                           135
  MALE                            88                           196
[1] 2 2
[1] FALSE
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    47 118
  AMP PEAK  8(7Q32.3) WILD-TYPE 137 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     47  118
  AMP PEAK  8(7Q32.3) WILD-TYPE  137  177
     clus
vv    AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  NO                           47                           137
  YES                         118                           177
[1] 2 2
[1] FALSE
D8V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  8(7Q32.3) MUTATED            77               49                55
  AMP PEAK  8(7Q32.3) WILD-TYPE         117               80               134
D8V6, multiclass
                   clus
vv                  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  ASTROCYTOMA                                77                           117
  OLIGOASTROCYTOMA                           49                            80
  OLIGODENDROGLIOMA                          55                           134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7Q32.3) MUTATED                                  1     4
  AMP PEAK  8(7Q32.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7Q32.3) MUTATED                          13   163
  AMP PEAK  8(7Q32.3) WILD-TYPE                         8   309
D8V7, multiclass
                                  clus
vv                                 AMP PEAK  8(7Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    163
                                  clus
vv                                 AMP PEAK  8(7Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      309
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED     9 166
  AMP PEAK  8(7Q32.3) WILD-TYPE  23 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED      9  166
  AMP PEAK  8(7Q32.3) WILD-TYPE   23  280
                        clus
vv                       AMP PEAK  8(7Q32.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         166
                        clus
vv                       AMP PEAK  8(7Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                23
  NOT HISPANIC OR LATINO                           280
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8Q24.13) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.13) MUTATED    75  24
  AMP PEAK  9(8Q24.13) WILD-TYPE 308 101
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            99                            409 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            24                            101 
$`AMP PEAK  9(8Q24.13) MUTATED`
TCGA-CS-6665 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-5277 
       51.55        36.36        40.18        37.38        46.95        50.86 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5143 
       78.28        30.21        39.78        37.45        18.51        46.06 
TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-5871 TCGA-DU-6399 TCGA-DU-6407 
       30.21        17.19        17.46        18.94        65.75        94.52 
TCGA-DU-6408 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7304 
      114.08        14.99         8.84       117.40        90.77        23.31 
TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 
        5.10        20.68        15.48        31.69        24.99        20.98 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC TCGA-DU-A7TI TCGA-E1-5303 
       17.98       139.04        84.33        37.38        38.89        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YW TCGA-E1-A7YY TCGA-FG-5962 
       41.13        79.99        57.93        36.82       146.14        47.77 
TCGA-FG-5964 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MY 
       52.21        41.33        15.35        14.96        38.27        23.70 
TCGA-FG-A70Y TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 
       28.54        16.54        17.42         6.54        24.26        40.34 
TCGA-HT-7482 TCGA-HT-7604 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7879 
      106.95       122.47        14.96        19.23        23.61         3.68 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A5R7 TCGA-HT-A614 
       16.24        63.55         0.10         0.23        20.22         2.70 
TCGA-HT-A616 TCGA-HT-A74J TCGA-HT-A74O TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        1.81        10.52         0.10         5.88         7.96         7.59 
TCGA-P5-A72W TCGA-QH-A6CW TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TY 
       10.42        13.61        16.50         9.90        87.12        35.38 
TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7QW 
       35.15        85.55        38.56        18.61        18.64        15.06 
TCGA-S9-A7QX TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH 
       18.54        65.39        30.44        25.38        23.80        15.98 
TCGA-TQ-A7RM TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 
       36.69        26.14        25.87        61.41        26.99        45.93 
TCGA-VM-A8CA TCGA-VM-A8CF TCGA-WY-A858 
       13.51        20.02        43.96 

$`AMP PEAK  9(8Q24.13) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       60.10         0.26        21.01        53.62         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       26.76        48.30        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       46.42        18.84        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       29.23        14.40        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F 
       16.18        19.96        63.88        24.59        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       54.25        23.21        13.71        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
      133.74        19.89        16.83         7.96         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7018 
       62.96       156.23       154.36       105.21         6.54        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       25.91        60.30        41.98         2.76        23.74        14.60 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        14.17        33.27        29.85 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       24.43        26.17        33.96        25.55        21.57        95.11 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7TB TCGA-DU-A7TD 
       22.29        11.41        26.76        21.30        51.52         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       44.42         0.56        50.14       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
      130.78        14.30        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       12.43        16.18        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
        0.76        32.45        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 
       39.48         0.23         0.20        25.48        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       14.93        42.54        18.44        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8189 
       20.09        28.34        13.68        14.24        16.01        22.52 
TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L 
       32.61        10.72        18.38        18.71        14.76        21.53 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        22.26        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 
        0.13         0.03         3.75         6.38        75.19        95.93 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      172.77         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        31.69         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        2.96        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         5.56        13.78        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       28.27        15.72         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 
       27.35         0.10         5.33        16.93        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.52        17.65         2.43        15.35        11.05        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       45.44        41.49        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54        24.92        31.63        12.76        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F6 TCGA-P5-A72U 
        7.99         2.37         2.30         9.44         1.28         0.23 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23        13.41         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X 
       14.53        16.34        16.73         1.91        16.70        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y 
       12.99        88.83        94.03        32.65        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TV 
       28.08         2.07        19.59        30.67        62.17        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       41.10        40.93        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WQ 
      135.22        84.99        31.10        19.86        26.47        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        20.68        28.37        27.16       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       20.48        54.77        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RF TCGA-TQ-A7RG 
       24.79        33.24        18.61        14.93        21.37        19.69 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        44.09        33.73        31.20        30.05 
TCGA-TQ-A7RU TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.93        31.36        43.20         0.10         7.89        39.16 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       13.32        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                        146.14                         211.17 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                         26.14                          21.30 
[1] "0.1 - 146.1 (26.1)" "0.0 - 211.2 (21.3)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    39  60
  AMP PEAK  9(8Q24.13) WILD-TYPE 189 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     39   60
  AMP PEAK  9(8Q24.13) WILD-TYPE  189  224
        clus
vv       AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  FEMALE                           39                            189
  MALE                             60                            224
[1] 2 2
[1] FALSE
D9V4, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    25  69
  AMP PEAK  9(8Q24.13) WILD-TYPE 159 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     25   69
  AMP PEAK  9(8Q24.13) WILD-TYPE  159  226
     clus
vv    AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  NO                            25                            159
  YES                           69                            226
[1] 2 2
[1] FALSE
D9V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  9(8Q24.13) MUTATED            47               29                23
  AMP PEAK  9(8Q24.13) WILD-TYPE         147              100               166
D9V6, multiclass
                   clus
vv                  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  ASTROCYTOMA                                 47                            147
  OLIGOASTROCYTOMA                            29                            100
  OLIGODENDROGLIOMA                           23                            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.13) MUTATED                                  0     0
  AMP PEAK  9(8Q24.13) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.13) MUTATED                           4    93
  AMP PEAK  9(8Q24.13) WILD-TYPE                        17   379
D9V7, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      93
                                  clus
vv                                 AMP PEAK  9(8Q24.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       379
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED     9  83
  AMP PEAK  9(8Q24.13) WILD-TYPE  23 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED      9   83
  AMP PEAK  9(8Q24.13) WILD-TYPE   23  363
                        clus
vv                       AMP PEAK  9(8Q24.13) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       AMP PEAK  9(8Q24.13) WILD-TYPE
  HISPANIC OR LATINO                                 23
  NOT HISPANIC OR LATINO                            363
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(9Q34.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(9Q34.3) MUTATED    36  10
  AMP PEAK 10(9Q34.3) WILD-TYPE 347 115
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           46                           462 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           10                           115 
$`AMP PEAK 10(9Q34.3) MUTATED`
TCGA-CS-6665 TCGA-DU-A76O TCGA-FG-A60K TCGA-FG-A87N TCGA-CS-5396 TCGA-CS-5397 
       51.55        17.16        17.82        18.64        53.62         6.38 
TCGA-CS-6290 TCGA-DB-A4XE TCGA-DB-A64R TCGA-DB-A64X TCGA-DH-5142 TCGA-DU-7010 
       37.38        37.45        31.40        18.51        63.88        14.99 
TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 
       18.94         5.10        23.74        21.40        19.13        14.17 
TCGA-DU-A5TT TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-A7Z3 TCGA-FG-A4MY TCGA-FG-A6J3 
       24.43        50.14        41.13        73.48        23.70        22.26 
TCGA-HT-7468 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7686 
        6.67        24.26         6.38       172.77         5.03        42.74 
TCGA-HT-7873 TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A74J TCGA-HW-8319 
       23.61         0.10        16.14        17.52        10.52        39.75 
TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7QW TCGA-TM-A84F TCGA-TM-A84H 
       41.10        38.56        19.86        15.06        59.05        30.44 
TCGA-TM-A84T TCGA-TQ-A7RM TCGA-TQ-A7RR TCGA-WY-A85E 
       23.80        36.69        25.87        20.81 

$`AMP PEAK 10(9Q34.3) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-E1-A7YN 
       46.88        46.72        31.82        42.05        62.01        23.90 
TCGA-FG-8187 TCGA-FG-A713 TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M 
       20.09        20.45        21.40        45.60        42.77        59.38 
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
      117.50         7.69        43.89        36.36        60.10        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6667 
        0.26        21.01        17.69        26.76        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.94        49.12       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        91.13        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       46.42        18.84        30.21        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S 
       31.63        24.20        25.48        30.12         5.98        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        14.40        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       30.74        16.18        19.96        46.06        24.59        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        2.40        11.47        62.96       156.23       154.36       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 
       10.36         7.96        94.32        44.02        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8166 
       23.31        41.98         2.76        14.60        20.68        16.96 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        33.27        29.85        31.69        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
      130.78        14.30        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       12.43        16.18        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 
        0.76        32.45        36.82       146.14        13.08       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       28.34        13.68        14.24        16.01        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       32.61        38.27        10.72        18.38        18.71        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 
       48.69         5.72        27.52         0.10        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 
       40.34        75.19        95.93       106.95         4.01        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 
       16.24         0.76        44.68         6.05         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
        0.49        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC 
       26.04         0.13        20.22         0.07        27.35         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61C TCGA-HT-A74H 
        2.70        16.93         1.81        16.83        17.65         2.43 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       68.32        69.27        35.44        40.01        42.54        24.92 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       31.63        12.76        28.87        20.71        19.00        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         7.99         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        9.44         5.88         7.96         7.59         1.28         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       32.65        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        18.77        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
      135.22        85.55        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX 
       19.99        20.02         8.19         2.04        20.68        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G 
       49.32        34.78        65.39        24.92        16.18        40.64 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       40.41        44.09        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        45.93        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                       172.77                        211.17 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                       23.655                        22.175 
[1] "0.1 - 172.8 (23.7)" "0.0 - 211.2 (22.2)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED    26  20
  AMP PEAK 10(9Q34.3) WILD-TYPE 202 264
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED     26   20
  AMP PEAK 10(9Q34.3) WILD-TYPE  202  264
        clus
vv       AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  FEMALE                          26                           202
  MALE                            20                           264
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED     8  35
  AMP PEAK 10(9Q34.3) WILD-TYPE 176 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED      8   35
  AMP PEAK 10(9Q34.3) WILD-TYPE  176  260
     clus
vv    AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  NO                            8                           176
  YES                          35                           260
[1] 2 2
[1] FALSE
D10V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 10(9Q34.3) MUTATED            24               13                 9
  AMP PEAK 10(9Q34.3) WILD-TYPE         170              116               180
D10V6, multiclass
                   clus
vv                  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  ASTROCYTOMA                                24                           170
  OLIGOASTROCYTOMA                           13                           116
  OLIGODENDROGLIOMA                           9                           180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(9Q34.3) MUTATED                                  1     1
  AMP PEAK 10(9Q34.3) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(9Q34.3) MUTATED                           2    40
  AMP PEAK 10(9Q34.3) WILD-TYPE                        19   432
D10V7, multiclass
                                  clus
vv                                 AMP PEAK 10(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     40
                                  clus
vv                                 AMP PEAK 10(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED     5  38
  AMP PEAK 10(9Q34.3) WILD-TYPE  27 408
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED      5   38
  AMP PEAK 10(9Q34.3) WILD-TYPE   27  408
                        clus
vv                       AMP PEAK 10(9Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       AMP PEAK 10(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                27
  NOT HISPANIC OR LATINO                           408
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(10P15.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(10P15.3) MUTATED    53  18
  AMP PEAK 11(10P15.3) WILD-TYPE 330 107
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            71                            437 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            18                            107 
$`AMP PEAK 11(10P15.3) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6666 TCGA-CS-6667 
       51.55        42.05        36.36        40.18        46.95        48.30 
TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-A4XE TCGA-DB-A75M TCGA-DH-A7UU TCGA-DH-A7UV 
      122.73        50.86        37.45        17.88        13.71        18.61 
TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 
       18.94        75.16       114.08       117.40        26.30        44.02 
TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-E1-5303 TCGA-E1-5304 
       23.31        29.85        31.69        24.99        67.46        41.13 
TCGA-E1-5322 TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YW TCGA-FG-6691 TCGA-FG-8185 
      130.78         3.65        12.43        36.82        41.33        14.24 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7476 
       23.70        21.53        28.54        40.11        16.54         6.54 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7873 TCGA-HT-7879 
       40.34       106.95       172.77        31.69        23.61         3.68 
TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7493 
        0.10         0.23        34.19         0.10        41.49        69.27 
TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-P5-A780 
       42.54        19.00         2.30         5.88        13.25         2.37 
TCGA-QH-A6XA TCGA-RY-A845 TCGA-S9-A6U0 TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A89Z 
       16.50        19.59        24.39         7.92        20.02        20.48 
TCGA-TM-A7CA TCGA-TM-A84H TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C8 
       34.78        30.44        15.98        44.09        61.41        45.93 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       13.32        43.96        39.88        43.40        20.81 

$`AMP PEAK 11(10P15.3) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O TCGA-E1-A7YN 
       46.88        46.72        31.82        62.01        17.16        23.90 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 
       20.09        17.82        20.45        18.64        21.40        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 
       42.77        59.38       117.50         7.69        43.89        60.10 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.26        21.01        53.62         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       37.38        49.94        49.12        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       18.84        30.21        39.78        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        23.21 
TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       17.46        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        8.45         6.81       182.33        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52         7.96         2.40        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      154.36        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7301 
       30.67        10.36         7.96        94.32        18.94        25.91 
TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       33.27        24.43        26.17        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       95.11        20.98        22.29        11.41        26.76        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 
       44.42        38.89         0.56        50.14        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
      134.27        78.21        95.57        14.30        29.13        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       19.46        16.18        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        32.45       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 
       52.21        36.82        18.77        14.93        42.54        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       13.68        16.01        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       10.72        18.38        18.71        14.76        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 
       22.26        10.78        36.66        48.69         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        0.10         6.67        11.54         0.13         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 
       17.42        24.26         6.38        75.19        95.93         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 
        2.43        10.52        15.35        11.05        56.58        45.44 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       68.32        35.44        39.75        40.01        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        28.87        20.71        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.71         7.99         2.37         9.44         7.96         7.59 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.23        10.42        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.70        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 
       30.87         5.46         9.90        28.08         2.07        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       36.82        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        14.07        36.13        26.93        23.51        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       31.59        18.71        54.77        48.33        49.32        65.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RM 
       23.80        21.37        19.69         2.04        40.41        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        31.36        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
        8.05        51.06        45.80        46.88        37.71 

  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                        172.77                         211.17 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                         30.44                          21.30 
[1] "0.1 - 172.8 (30.4)" "0.0 - 211.2 (21.3)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    26  45
  AMP PEAK 11(10P15.3) WILD-TYPE 202 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     26   45
  AMP PEAK 11(10P15.3) WILD-TYPE  202  239
        clus
vv       AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  FEMALE                           26                            202
  MALE                             45                            239
[1] 2 2
[1] FALSE
D11V4, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    19  48
  AMP PEAK 11(10P15.3) WILD-TYPE 165 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     19   48
  AMP PEAK 11(10P15.3) WILD-TYPE  165  247
     clus
vv    AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  NO                            19                            165
  YES                           48                            247
[1] 2 2
[1] FALSE
D11V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 11(10P15.3) MUTATED            38               24                 9
  AMP PEAK 11(10P15.3) WILD-TYPE         156              105               180
D11V6, multiclass
                   clus
vv                  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  ASTROCYTOMA                                 38                            156
  OLIGOASTROCYTOMA                            24                            105
  OLIGODENDROGLIOMA                            9                            180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(10P15.3) MUTATED                                  0     0
  AMP PEAK 11(10P15.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(10P15.3) MUTATED                           3    68
  AMP PEAK 11(10P15.3) WILD-TYPE                        18   404
D11V7, multiclass
                                  clus
vv                                 AMP PEAK 11(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      68
                                  clus
vv                                 AMP PEAK 11(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       404
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED     7  57
  AMP PEAK 11(10P15.3) WILD-TYPE  25 389
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED      7   57
  AMP PEAK 11(10P15.3) WILD-TYPE   25  389
                        clus
vv                       AMP PEAK 11(10P15.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       AMP PEAK 11(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            389
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(11Q24.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(11Q24.1) MUTATED    67  20
  AMP PEAK 12(11Q24.1) WILD-TYPE 316 105
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            87                            421 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            20                            105 
$`AMP PEAK 12(11Q24.1) MUTATED`
TCGA-DB-A4XC TCGA-HW-7490 TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A4XB 
       46.72        45.60        53.62        50.86        46.42        30.21 
TCGA-DB-A4XD TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A75L TCGA-DH-5144 
       39.78        24.20         5.98        29.23        11.24        24.59 
TCGA-DH-A66D TCGA-DH-A7UT TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       27.81        17.46         6.74         6.81       182.33        18.94 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-7015 
      211.17        52.11        46.06         1.22        94.52        90.77 
TCGA-DU-7018 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       30.67        18.94        25.91        23.31        41.98         2.76 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5318 
       24.43        24.99        20.98        22.29        41.13        78.21 
TCGA-E1-A7Z3 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-8191 TCGA-FG-A60L TCGA-HT-7470 
       73.48        47.77        15.35        32.61        21.53        40.11 
TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 TCGA-HT-7676 TCGA-HT-7684 
        3.75         5.03       122.47         3.16         0.16         6.05 
TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-8109 TCGA-HT-A74H TCGA-HT-A74K TCGA-HW-8319 
       31.69        17.52         5.56         2.43        15.35        39.75 
TCGA-HW-8321 TCGA-P5-A5EV TCGA-P5-A72W TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ 
       42.54         0.23        10.42         2.53        15.85         9.17 
TCGA-QH-A6X9 TCGA-RY-A840 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TY 
        1.91        28.08        19.59        87.12        41.10        35.38 
TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WN TCGA-S9-A7IZ TCGA-S9-A7QY TCGA-S9-A7QZ 
       75.25        38.56        26.47        19.99        28.37        27.16 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RJ 
       31.59        20.48        24.92        28.08        24.16        40.41 
TCGA-TQ-A7RN TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CF 
       33.73        61.41        26.99        45.93        13.51        20.02 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       45.80        46.88        20.81 

$`AMP PEAK 12(11Q24.1) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 
       60.10        40.18         0.26        21.01         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       26.76        37.38        46.95        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        91.13 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A4XF 
       44.52        36.56        78.28        18.84        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S 
       72.95        31.63        25.48        30.12        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O 
       27.81        14.40        18.51        12.10        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66F 
       16.18        19.96        63.88        46.06        30.21        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        23.21        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5872 TCGA-DU-5874 
       14.56        17.46        13.38         8.45        17.49        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        16.83       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        2.40        11.47        62.96       156.23       154.36        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54         8.84       117.40        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 
        7.96        94.32        44.02        60.30         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TY 
       14.17        33.27        29.85        31.69        26.17        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       25.55        21.57        95.11        11.41        26.76        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       44.42        38.89         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
       57.93       134.27        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
       93.21         3.65        19.46        12.43        16.18        21.30 
TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       75.02        51.88        15.32         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        13.08       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       42.54        41.33        18.44        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       20.09        28.34        13.68        14.24        16.01        14.96 
TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       36.66        48.69         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 
       11.54         0.13         0.03        16.54        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
      172.77         4.01        29.85        23.18         4.57        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
       16.24         0.76        44.68        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.14        16.83        17.52        17.65 
TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       10.52        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       68.32        69.27        35.44        40.01        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        28.87        20.71        19.00        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        7.96         7.59         1.28         0.23        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V 
       19.20         3.45         2.37         4.41        15.16        12.62 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
       13.41        10.29        14.53        16.34        16.73        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.70        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS 
       30.87         5.46         9.90         2.07        30.67        62.17 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        40.93        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WO 
      135.22        85.55        84.99        31.10        19.86        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
      169.84        10.39        99.06        30.05        98.63        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       54.77        48.33        49.32        34.78        65.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        40.64        30.44        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RO TCGA-TQ-A7RP 
       15.98         2.04        44.09        36.69        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CB 
       26.14        25.87        33.93        31.36        43.20         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        39.16        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85D 
       37.71 

  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                        211.17                         172.77 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                         26.99                          20.71 
[1] "0.2 - 211.2 (27.0)" "0.0 - 172.8 (20.7)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    42  45
  AMP PEAK 12(11Q24.1) WILD-TYPE 186 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     42   45
  AMP PEAK 12(11Q24.1) WILD-TYPE  186  239
        clus
vv       AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  FEMALE                           42                            186
  MALE                             45                            239
[1] 2 2
[1] FALSE
D12V4, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    32  53
  AMP PEAK 12(11Q24.1) WILD-TYPE 152 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     32   53
  AMP PEAK 12(11Q24.1) WILD-TYPE  152  242
     clus
vv    AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  NO                            32                            152
  YES                           53                            242
[1] 2 2
[1] FALSE
D12V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 12(11Q24.1) MUTATED            33               18                36
  AMP PEAK 12(11Q24.1) WILD-TYPE         161              111               153
D12V6, multiclass
                   clus
vv                  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  ASTROCYTOMA                                 33                            161
  OLIGOASTROCYTOMA                            18                            111
  OLIGODENDROGLIOMA                           36                            153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(11Q24.1) MUTATED                                  0     0
  AMP PEAK 12(11Q24.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(11Q24.1) MUTATED                           4    80
  AMP PEAK 12(11Q24.1) WILD-TYPE                        17   392
D12V7, multiclass
                                  clus
vv                                 AMP PEAK 12(11Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      80
                                  clus
vv                                 AMP PEAK 12(11Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED     5  74
  AMP PEAK 12(11Q24.1) WILD-TYPE  27 372
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED      5   74
  AMP PEAK 12(11Q24.1) WILD-TYPE   27  372
                        clus
vv                       AMP PEAK 12(11Q24.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       AMP PEAK 12(11Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                 27
  NOT HISPANIC OR LATINO                            372
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(12P13.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(12P13.32) MUTATED    44  28
  AMP PEAK 13(12P13.32) WILD-TYPE 339  97
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             72                             436 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             28                              97 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-DB-A4XC TCGA-CS-4943 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 
       46.72        36.36        81.96        47.93        50.86        78.28 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A64P TCGA-DH-A669 TCGA-DU-6395 TCGA-DU-6396 
       30.21        37.45        30.12        30.21        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 
       65.75         1.22        11.64       114.08        62.96       156.23 
TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       44.02        23.31        19.13        33.27        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TI TCGA-E1-5303 
       26.17        33.96       139.04        84.33        38.89        67.46 
TCGA-E1-5304 TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       41.13        93.21         3.65        51.88        15.32         0.76 
TCGA-E1-A7YW TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 
       36.82        36.82        42.54        41.33        15.35        13.68 
TCGA-FG-8185 TCGA-FG-8191 TCGA-FG-A6J3 TCGA-FG-A711 TCGA-HT-7469 TCGA-HT-7473 
       14.24        32.61        22.26        48.69        11.54        16.54 
TCGA-HT-7478 TCGA-HT-7604 TCGA-HT-7686 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
        6.38       122.47        42.74        23.61         3.68        11.28 
TCGA-HT-8018 TCGA-HT-A614 TCGA-HW-A5KM TCGA-QH-A6CV TCGA-RY-A83Z TCGA-S9-A6UA 
       37.87         2.70        20.71        14.53         9.90         5.85 
TCGA-S9-A6WO TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R7 TCGA-TM-A84I 
       18.61        19.99        20.02        18.54        98.63        28.08 
TCGA-TQ-A7RK TCGA-TQ-A7RR TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       44.09        25.87        43.96        39.88        45.80        20.81 

$`AMP PEAK 13(12P13.32) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       49.12       122.73        75.25        72.92        91.13        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       36.56        46.42        18.84        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        24.20        25.48         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        63.88        46.06 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       24.59        27.81        17.19        17.19        54.25        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
       17.49        15.16       211.17        52.11        22.42        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96         2.40        11.47       154.36        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7302 
       10.36         7.96        94.32        18.94        25.91        60.30 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TW 
       21.40        16.96        15.48        14.17        29.85        24.99 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76        21.30        17.98        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42         0.56        50.14        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YJ 
       78.21        95.57       130.78        14.30        29.13        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YY 
       12.43        16.18        21.30        75.02        32.45       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 
        0.20        47.77        25.48        52.21        18.77        14.93 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        17.88        22.55        20.61        20.09        28.34 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        14.96        22.52        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       28.54        10.78        36.66         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 
        6.67        40.11         0.13         0.03         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54        24.26        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      172.77         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        0.13         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55         0.10        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        5.33        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       28.87        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        7.99         2.37         2.30         9.44         5.88         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.59         1.28         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        40.93        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       29.85        32.61        35.15        98.24        95.93       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       19.86        26.47        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       26.93        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       26.14        33.93        61.41        26.99        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       43.20        13.51         0.10         7.89        39.16        20.02 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       13.32        43.40        46.88        37.71 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                           0.76                            0.03 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         156.23                          211.17 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                          32.94                           20.83 
[1] "0.8 - 156.2 (32.9)" "0.0 - 211.2 (20.8)"
[1] "hr=" "1.3"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    26  46
  AMP PEAK 13(12P13.32) WILD-TYPE 202 238
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     26   46
  AMP PEAK 13(12P13.32) WILD-TYPE  202  238
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            26                             202
  MALE                              46                             238
[1] 2 2
[1] FALSE
D13V4, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    18  52
  AMP PEAK 13(12P13.32) WILD-TYPE 166 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     18   52
  AMP PEAK 13(12P13.32) WILD-TYPE  166  243
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                             18                             166
  YES                            52                             243
[1] 2 2
[1] FALSE
D13V5, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  AMP PEAK 13(12P13.32) MUTATED            32               21
  AMP PEAK 13(12P13.32) WILD-TYPE         162              108
                                 vv
clus                              OLIGODENDROGLIOMA
  AMP PEAK 13(12P13.32) MUTATED                  19
  AMP PEAK 13(12P13.32) WILD-TYPE               170
D13V6, multiclass
                   clus
vv                  AMP PEAK 13(12P13.32) MUTATED
  ASTROCYTOMA                                  32
  OLIGOASTROCYTOMA                             21
  OLIGODENDROGLIOMA                            19
                   clus
vv                  AMP PEAK 13(12P13.32) WILD-TYPE
  ASTROCYTOMA                                   162
  OLIGOASTROCYTOMA                              108
  OLIGODENDROGLIOMA                             170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(12P13.32) MUTATED                                  0     1
  AMP PEAK 13(12P13.32) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(12P13.32) MUTATED                           4    67
  AMP PEAK 13(12P13.32) WILD-TYPE                        17   405
D13V7, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       67
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                        405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     3  63
  AMP PEAK 13(12P13.32) WILD-TYPE  29 383
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      3   63
  AMP PEAK 13(12P13.32) WILD-TYPE   29  383
                        clus
vv                       AMP PEAK 13(12P13.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            63
                        clus
vv                       AMP PEAK 13(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  29
  NOT HISPANIC OR LATINO                             383
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q14.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q14.1) MUTATED    16  21
  AMP PEAK 14(12Q14.1) WILD-TYPE 367 104
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            37                            471 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            21                            104 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-CS-6665 TCGA-CS-4941 TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 
       51.55         7.69        30.21         1.22        11.64        14.99 
TCGA-DU-7013 TCGA-DU-7298 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A7TA 
        8.84        18.94        19.13        24.43        33.96        84.33 
TCGA-E1-5305 TCGA-E1-5318 TCGA-E1-A7YD TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV 
       79.99        78.21        14.30        16.18        51.88        32.45 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-8563 TCGA-HT-A5RC 
       15.35        17.88        22.26        10.78        28.27         5.33 
TCGA-HT-A614 TCGA-HT-A61B TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A72U TCGA-QH-A6CV 
        2.70        17.52        19.00         2.30         0.23        14.53 
TCGA-S9-A6UA TCGA-S9-A7IZ TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
        5.85        19.99        10.39        54.77        24.92        28.08 
TCGA-VW-A8FI 
        8.05 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 
       45.60        42.77        59.38       117.50        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       46.06        24.59        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       23.21        17.46        13.71        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        87.45         7.04 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        2.40        11.47        62.96       156.23       154.36       105.21 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        16.96        15.48        14.17        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       31.69        26.17        24.99        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
       20.98        22.29        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
      139.04        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        41.13        57.93       134.27 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW 
       12.43        21.30        75.02        15.32         0.76        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
      146.14        13.08        73.48       145.05        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 
       18.77        14.93        42.54        41.33        18.44        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        28.34        13.68        14.24        16.01 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       28.54        36.66        48.69         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
       27.35         0.10        16.93         1.81        16.14        16.83 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       28.87        20.71        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        7.99         2.37         9.44         5.88         7.96         7.59 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       32.65        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       40.93        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        35.15        98.24        95.93       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       26.93        23.51        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 
       15.06        18.54        28.37        27.16       169.84        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        20.48        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        65.39        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       31.36        45.93        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        23.47        37.05        16.01        23.21 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          0.23                           0.03 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         84.33                         211.17 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         17.88                          23.21 
[1] "0.2 - 84.3 (17.9)"  "0.0 - 211.2 (23.2)"
[1] "hr=" "3.9"
D14V2, continuous
D14V3, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    17  20
  AMP PEAK 14(12Q14.1) WILD-TYPE 211 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     17   20
  AMP PEAK 14(12Q14.1) WILD-TYPE  211  264
        clus
vv       AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  FEMALE                           17                            211
  MALE                             20                            264
[1] 2 2
[1] FALSE
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     7  28
  AMP PEAK 14(12Q14.1) WILD-TYPE 177 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      7   28
  AMP PEAK 14(12Q14.1) WILD-TYPE  177  267
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                             7                            177
  YES                           28                            267
[1] 2 2
[1] FALSE
D14V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 14(12Q14.1) MUTATED            22                5                10
  AMP PEAK 14(12Q14.1) WILD-TYPE         172              124               179
D14V6, multiclass
                   clus
vv                  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  ASTROCYTOMA                                 22                            172
  OLIGOASTROCYTOMA                             5                            124
  OLIGODENDROGLIOMA                           10                            179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(12Q14.1) MUTATED                                  0     1
  AMP PEAK 14(12Q14.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q14.1) MUTATED                           3    33
  AMP PEAK 14(12Q14.1) WILD-TYPE                        18   439
D14V7, multiclass
                                  clus
vv                                 AMP PEAK 14(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      33
                                  clus
vv                                 AMP PEAK 14(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       439
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     1  36
  AMP PEAK 14(12Q14.1) WILD-TYPE  31 410
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      1   36
  AMP PEAK 14(12Q14.1) WILD-TYPE   31  410
                        clus
vv                       AMP PEAK 14(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       AMP PEAK 14(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 31
  NOT HISPANIC OR LATINO                            410
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q34) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(13Q34) MUTATED    17   4
  AMP PEAK 15(13Q34) WILD-TYPE 366 121
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          21                          487 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                           4                          121 
$`AMP PEAK 15(13Q34) MUTATED`
TCGA-DB-5277 TCGA-DU-5853 TCGA-DU-7015 TCGA-DU-7301 TCGA-DU-A5TT TCGA-DU-A5TU 
       50.86        13.38        90.77        25.91        24.43        26.17 
TCGA-DU-A5TY TCGA-HT-7476 TCGA-HT-7604 TCGA-HT-7611 TCGA-HT-7688 TCGA-HT-7873 
       33.96         6.54       122.47        57.60        31.69        23.61 
TCGA-HT-8563 TCGA-HT-A5R7 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-S9-A89Z TCGA-TM-A7C3 
       28.27        20.22         2.53         1.91        20.48        54.77 
TCGA-TM-A84T TCGA-TQ-A7RM TCGA-VM-A8CA 
       23.80        36.69        13.51 

$`AMP PEAK 15(13Q34) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       43.89        36.36        60.10        40.18         0.26        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 
       53.62         6.38        17.69        26.76        37.38        46.95 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
       48.30        49.94        49.12       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        91.13        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       63.88        46.06        24.59        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        23.21        17.46        13.71        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
       18.02        14.56        17.46         6.74         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       18.94        44.02        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        33.27        29.85        31.69 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       24.99        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO 
        3.65        19.46        12.43        16.18        21.30        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       18.38        18.71        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 
        0.13         0.03        16.54         3.75        17.42        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        56.09         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS 
       13.78         0.23        29.59        34.19        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       39.75        40.01        42.54        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       28.87        20.71        19.00        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.96         7.59         1.28         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23        13.41         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        31.10        19.86        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       98.63        31.59        18.71        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       65.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        21.37        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       40.41        44.09        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       25.87        33.93        61.41        26.99        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       43.20         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                        1.91                         0.03 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      122.47                       211.17 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                       25.91                        21.57 
[1] "1.9 - 122.5 (25.9)" "0.0 - 211.2 (21.6)"
[1] "hr=" "1.3"
D15V2, continuous
D15V3, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     9  13
  AMP PEAK 15(13Q34) WILD-TYPE 219 271
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      9   13
  AMP PEAK 15(13Q34) WILD-TYPE  219  271
        clus
vv       AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  FEMALE                          9                          219
  MALE                           13                          271
[1] 2 2
[1] FALSE
D15V4, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     8  14
  AMP PEAK 15(13Q34) WILD-TYPE 176 281
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      8   14
  AMP PEAK 15(13Q34) WILD-TYPE  176  281
     clus
vv    AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  NO                           8                          176
  YES                         14                          281
[1] 2 2
[1] FALSE
D15V5, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 15(13Q34) MUTATED            10                6                 6
  AMP PEAK 15(13Q34) WILD-TYPE         184              123               183
D15V6, multiclass
                   clus
vv                  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  ASTROCYTOMA                               10                          184
  OLIGOASTROCYTOMA                           6                          123
  OLIGODENDROGLIOMA                          6                          183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q34) MUTATED                                  0     0
  AMP PEAK 15(13Q34) WILD-TYPE                                1     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q34) MUTATED                           1    20
  AMP PEAK 15(13Q34) WILD-TYPE                        20   452
D15V7, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    20
                                  clus
vv                                 AMP PEAK 15(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     452
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     2  19
  AMP PEAK 15(13Q34) WILD-TYPE  30 427
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      2   19
  AMP PEAK 15(13Q34) WILD-TYPE   30  427
                        clus
vv                       AMP PEAK 15(13Q34) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         19
                        clus
vv                       AMP PEAK 15(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               30
  NOT HISPANIC OR LATINO                          427
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(15Q26.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.3) MUTATED     7  12
  AMP PEAK 16(15Q26.3) WILD-TYPE 376 113
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            19                            489 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            12                            113 
$`AMP PEAK 16(15Q26.3) MUTATED`
TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5277 TCGA-DU-5852 TCGA-DU-7306 TCGA-E1-5304 
       36.36        46.95        50.86         6.74        41.98        41.13 
TCGA-E1-A7YK TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-FG-A4MY TCGA-HT-7470 TCGA-HT-8108 
       12.43        51.88        32.45        23.70        40.11         2.50 
TCGA-HW-8319 TCGA-P5-A780 TCGA-S9-A6UA TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-TM-A84B 
       39.75         2.37         5.85         7.92        19.99        24.92 
TCGA-TQ-A7RR 
       25.87 

$`AMP PEAK 16(15Q26.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       43.89        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 
        6.38        17.69        26.76        37.38        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       91.13        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       30.21        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        63.88        46.06 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       24.59        30.21        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       23.21        17.46        13.71        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       17.46        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         2.40        11.47        62.96       156.23       154.36 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       44.02        25.91        60.30        23.31         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 
       20.98        22.29        11.41        26.76        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       38.89         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO 
       93.21         3.65        19.46        16.18        21.30        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       20.09        28.34        13.68        14.24        16.01        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        21.53        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       10.78        36.66        48.69         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       33.01        12.23         6.25         0.10         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       69.27        35.44        40.01        42.54        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        28.87        20.71        19.00        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         7.99         2.37         2.30         9.44 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.96         7.59         1.28         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23        19.20         3.45         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23        13.41         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50        16.70 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
       18.64        14.07        36.13        26.93        23.51        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        65.39        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       30.05        26.14        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       45.93        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          2.37                           0.03 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         51.88                         211.17 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         25.87                          22.06 
[1] "2.4 - 51.9 (25.9)"  "0.0 - 211.2 (22.1)"
[1] "hr=" "3.5"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     9  10
  AMP PEAK 16(15Q26.3) WILD-TYPE 219 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      9   10
  AMP PEAK 16(15Q26.3) WILD-TYPE  219  274
        clus
vv       AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  FEMALE                            9                            219
  MALE                             10                            274
[1] 2 2
[1] FALSE
D16V4, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     5  14
  AMP PEAK 16(15Q26.3) WILD-TYPE 179 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      5   14
  AMP PEAK 16(15Q26.3) WILD-TYPE  179  281
     clus
vv    AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  NO                             5                            179
  YES                           14                            281
[1] 2 2
[1] FALSE
D16V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 16(15Q26.3) MUTATED            11                5                 3
  AMP PEAK 16(15Q26.3) WILD-TYPE         183              124               186
D16V6, multiclass
                   clus
vv                  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  ASTROCYTOMA                                 11                            183
  OLIGOASTROCYTOMA                             5                            124
  OLIGODENDROGLIOMA                            3                            186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(15Q26.3) MUTATED                                  0     0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.3) MUTATED                           1    18
  AMP PEAK 16(15Q26.3) WILD-TYPE                        20   454
D16V7, multiclass
                                  clus
vv                                 AMP PEAK 16(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      18
                                  clus
vv                                 AMP PEAK 16(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       454
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     2  16
  AMP PEAK 16(15Q26.3) WILD-TYPE  30 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      2   16
  AMP PEAK 16(15Q26.3) WILD-TYPE   30  430
                        clus
vv                       AMP PEAK 16(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       AMP PEAK 16(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 30
  NOT HISPANIC OR LATINO                            430
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17Q25.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(17Q25.1) MUTATED    29  14
  AMP PEAK 17(17Q25.1) WILD-TYPE 354 111
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            43                            465 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            14                            111 
$`AMP PEAK 17(17Q25.1) MUTATED`
TCGA-CS-6665 TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A64P TCGA-DB-A64Q TCGA-DH-5140 
       51.55        30.21        33.57        30.12         5.98        19.96 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-6399 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7304 
       30.21        17.19        65.75        14.99         8.84        23.31 
TCGA-DU-A6S7 TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YO TCGA-F6-A8O4 TCGA-FG-5962 
       20.98        41.13        14.30        75.02         0.20        47.77 
TCGA-FG-7634 TCGA-FG-A60J TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-8010 TCGA-HT-A61C 
       15.35        14.76         5.72        24.26         1.64        17.65 
TCGA-IK-7675 TCGA-P5-A736 TCGA-QH-A6CV TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6U1 
       19.00         7.56        14.53        28.08        62.17        25.81 
TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84F 
        5.85        85.55        31.10        19.86        20.02        59.05 
TCGA-TM-A84H TCGA-TM-A84M TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-VM-A8CA TCGA-VM-A8CH 
       30.44        24.79        44.09        36.69        13.51        23.47 
TCGA-VW-A8FI 
        8.05 

$`AMP PEAK 17(17Q25.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       36.36        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        6.38        17.69        26.76        37.38        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.94        49.12       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        91.13        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH 
       46.42        18.84        39.78        37.45        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       24.20        25.48        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       14.40        18.51        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66G 
       16.18        63.88        46.06        24.59        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        23.21        17.46        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        75.16        46.06         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         2.40        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      154.36       105.21         6.54       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
       24.99        33.96        25.55        21.57        95.11        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        29.13        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       12.43        16.18        21.30        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       32.35        39.48         0.23        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        42.54        41.33        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.38        18.71        23.70        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FN-7833 
       22.26        28.54        10.78        36.66        48.69        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.14        16.83        17.52         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54        24.92 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 
       31.63        12.76        28.87        20.71        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         7.99         2.37         2.30         9.44 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.96         7.59         1.28         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23        13.41         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50        16.70        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y 
       12.99        88.83        94.03        32.65        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
        9.90         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 
       41.10        40.93        35.38        36.82        24.39        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        35.15        98.24        95.93       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
      135.22        38.56        84.99        26.47        18.61        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84I 
       34.78        65.39        24.92        16.18        40.64        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
       61.41        26.99        31.36        45.93        43.20         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        39.16        20.02        37.05        16.01        23.21 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         85.55                         211.17 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         23.31                          22.29 
[1] "0.2 - 85.5 (23.3)"  "0.0 - 211.2 (22.3)"
[1] "hr=" "1.8"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED    17  26
  AMP PEAK 17(17Q25.1) WILD-TYPE 211 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED     17   26
  AMP PEAK 17(17Q25.1) WILD-TYPE  211  258
        clus
vv       AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  FEMALE                           17                            211
  MALE                             26                            258
[1] 2 2
[1] FALSE
D17V4, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED    15  27
  AMP PEAK 17(17Q25.1) WILD-TYPE 169 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED     15   27
  AMP PEAK 17(17Q25.1) WILD-TYPE  169  268
     clus
vv    AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  NO                            15                            169
  YES                           27                            268
[1] 2 2
[1] FALSE
D17V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 17(17Q25.1) MUTATED            21                8                14
  AMP PEAK 17(17Q25.1) WILD-TYPE         173              121               175
D17V6, multiclass
                   clus
vv                  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  ASTROCYTOMA                                 21                            173
  OLIGOASTROCYTOMA                             8                            121
  OLIGODENDROGLIOMA                           14                            175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(17Q25.1) MUTATED                                  0     2
  AMP PEAK 17(17Q25.1) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q25.1) MUTATED                           0    38
  AMP PEAK 17(17Q25.1) WILD-TYPE                        21   434
D17V7, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      38
                                  clus
vv                                 AMP PEAK 17(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       434
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED     4  35
  AMP PEAK 17(17Q25.1) WILD-TYPE  28 411
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED      4   35
  AMP PEAK 17(17Q25.1) WILD-TYPE   28  411
                        clus
vv                       AMP PEAK 17(17Q25.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       AMP PEAK 17(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 28
  NOT HISPANIC OR LATINO                            411
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(19P13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(19P13.3) MUTATED    98  29
  AMP PEAK 18(19P13.3) WILD-TYPE 285  96
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           127                            381 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                            29                             96 
$`AMP PEAK 18(19P13.3) MUTATED`
TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-R8-A73M TCGA-CS-5395 
       31.82        62.01        20.09        17.82        59.38        21.01 
TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-5278 
       53.62        17.69        26.76        49.94        75.25        91.13 
TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       39.78        72.95        31.63        24.20        30.12        31.40 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75L TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 
       27.81        14.40        11.24        63.88        24.59        30.21 
TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       17.19        13.71         8.45        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 
       46.06         1.22         7.04        16.83       154.36        90.77 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A6S2 TCGA-DU-A6S6 
       26.30        18.94        41.98        21.40        25.55        95.11 
TCGA-DU-A76K TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-A7YJ TCGA-E1-A7YL 
       11.41         0.56        41.13        78.21        19.46        16.18 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7643 
       75.02        15.32        47.77        18.44        22.55        20.09 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Y TCGA-FG-A710 
       16.01        14.96        10.72        18.38        28.54        36.66 
TCGA-FG-A87Q TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7480 TCGA-HT-7483 
        5.72         6.67        11.54         0.03        75.19       172.77 
TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7695 TCGA-HT-7860 
        4.57        22.06        44.68         0.10        14.53         0.49 
TCGA-HT-7873 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5RA 
       23.61         0.33         3.72         9.40        12.23        27.35 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A61B TCGA-HW-7495 TCGA-HW-8322 TCGA-KT-A7W1 
        5.33        16.93        17.52        35.44        24.92        14.40 
TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ 
        9.44         0.23        10.95        15.85        14.53         9.17 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-RY-A83X TCGA-RY-A83Y 
       16.70        11.08        88.83        94.03        30.87         5.46 
TCGA-RY-A840 TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6UB 
       28.08        18.77        40.93        35.38        29.85       123.65 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
      135.22        38.56        19.86        19.99         8.19         2.04 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C3 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84G 
       27.16       169.84        54.77        65.39        24.92        40.64 
TCGA-TM-A84M TCGA-TM-A84Q TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RP 
       24.79        25.38        19.69         2.04        33.73        30.05 
TCGA-TQ-A7RQ TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS TCGA-W9-A837 
       26.14        13.51         0.10        39.16        23.21        51.06 
TCGA-WY-A85E 
       20.81 

$`AMP PEAK 18(19P13.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-E1-A7YN 
       51.55        46.88        46.72        42.05        17.16        23.90 
TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-CS-4938 
       20.45        18.64        21.40        45.60        42.77       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 
        7.69        43.89        36.36        60.10        40.18         0.26 
TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 
        6.38        37.38        46.95        48.30        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 
       81.96        47.93        72.92        50.86        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        46.42        18.84        30.21        37.45        33.57 
TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       25.48         5.98        27.45        29.23        18.51        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-A66D 
       17.88        30.74        16.18        19.96        46.06        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        23.21        17.46        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46         6.74        13.38         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       18.94        17.49       211.17        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
       87.45        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
        7.96         2.40        11.47        62.96       156.23        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 
      105.21         6.54         8.84       117.40        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        44.02        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
        2.76         5.10        23.74        14.60        20.68        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 
       24.43        26.17        24.99        33.96        21.57        20.98 
TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       22.29        26.76        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
       51.52        37.38         7.50        44.42        38.89        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 
       67.46        79.99        57.93       134.27        95.57       130.78 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YM 
       14.30        29.13        93.21         3.65        12.43        21.30 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       41.33        15.35        17.88        20.61        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.24        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.76        21.53        15.02        16.44        22.26        10.78 
TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 
       48.69        27.52         0.10        40.11         0.13        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       95.93       106.95         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
      122.47        17.29         3.16        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 
        0.23        14.27         0.16        16.24         0.76         6.05 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       50.63        37.15         0.13         3.68         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64        16.24        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61C 
        0.10         2.70         1.81        16.14        16.83        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
       45.44        41.49        68.32        69.27        39.75        40.01 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       42.54        31.63        12.76        28.87        20.71        19.00 
TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         7.99         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.96         7.59         1.28        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       11.64         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       19.20         3.45         2.37         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX 
       12.62        14.04        19.33        14.83        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
       13.41        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A870 TCGA-R8-A6MO TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 
       16.50        12.99        32.65         9.90         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TZ TCGA-S9-A6U0 
       30.67        62.17        87.12        41.10        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       25.81        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       75.25        85.55        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.64        14.07        36.13         7.92        26.93        23.51 
TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 
       20.02        20.68        15.06        18.54        28.37        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        20.48 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       48.33        49.32        34.78        16.18        59.05        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       28.08        24.16        40.83        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       23.80        21.37        15.98        40.41        44.09        36.69 
TCGA-TQ-A7RO TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       31.20        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
       45.93        43.20         7.89        20.02        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       16.01         8.05        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                        172.77                         211.17 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                         22.55                          22.26 
[1] "0.0 - 172.8 (22.6)" "0.1 - 211.2 (22.3)"
[1] "hr=" "1.2"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    54  75
  AMP PEAK 18(19P13.3) WILD-TYPE 174 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     54   75
  AMP PEAK 18(19P13.3) WILD-TYPE  174  209
        clus
vv       AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  FEMALE                           54                            174
  MALE                             75                            209
[1] 2 2
[1] FALSE
D18V4, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    60  62
  AMP PEAK 18(19P13.3) WILD-TYPE 124 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     60   62
  AMP PEAK 18(19P13.3) WILD-TYPE  124  233
     clus
vv    AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  NO                            60                            124
  YES                           62                            233
[1] 2 2
[1] FALSE
D18V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 18(19P13.3) MUTATED            26               29                74
  AMP PEAK 18(19P13.3) WILD-TYPE         168              100               115
D18V6, multiclass
                   clus
vv                  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  ASTROCYTOMA                                 26                            168
  OLIGOASTROCYTOMA                            29                            100
  OLIGODENDROGLIOMA                           74                            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(19P13.3) MUTATED                                  0     2
  AMP PEAK 18(19P13.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(19P13.3) MUTATED                           7   116
  AMP PEAK 18(19P13.3) WILD-TYPE                        14   356
D18V7, multiclass
                                  clus
vv                                 AMP PEAK 18(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                     116
                                  clus
vv                                 AMP PEAK 18(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    11 112
  AMP PEAK 18(19P13.3) WILD-TYPE  21 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     11  112
  AMP PEAK 18(19P13.3) WILD-TYPE   21  334
                        clus
vv                       AMP PEAK 18(19P13.3) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       AMP PEAK 18(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(XP11.22) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(XP11.22) MUTATED    40   8
  AMP PEAK 19(XP11.22) WILD-TYPE 343 117
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                            48                            460 
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                             8                            117 
$`AMP PEAK 19(XP11.22) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-FG-A713 TCGA-FG-A87N TCGA-CS-6667 TCGA-DB-5277 
       51.55        42.05        20.45        18.64        48.30        50.86 
TCGA-DB-5281 TCGA-DB-A75L TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7014 TCGA-DU-A5TP 
       78.28        11.24        18.94        94.52       117.40        33.27 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-E1-5302 TCGA-E1-5318 TCGA-E1-A7YK TCGA-E1-A7Z4 
       31.69        24.43        50.14        78.21        12.43       145.05 
TCGA-FG-7636 TCGA-FG-8185 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 
       17.88        14.24        17.42         6.54        24.26        45.99 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-A616 
       31.69        14.96        63.55        12.23         0.10         1.81 
TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ TCGA-P5-A72W 
       10.52         0.10        69.27        42.54         2.30        10.42 
TCGA-QH-A6CV TCGA-RY-A83Z TCGA-S9-A7QX TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RR 
       14.53         9.90        18.54        40.41        44.09        25.87 
TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-VM-A8CF TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       61.41        45.93        20.02        39.88        45.80        20.81 

$`AMP PEAK 19(XP11.22) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O TCGA-E1-A7YN 
       46.88        46.72        31.82        62.01        17.16        23.90 
TCGA-FG-8187 TCGA-FG-A60K TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M 
       20.09        17.82        21.40        45.60        42.77        59.38 
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
      117.50         7.69        43.89        36.36        60.10        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.26        21.01        53.62         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        46.95        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       12.10        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       46.06        24.59        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        23.21        17.46        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         2.40        11.47        62.96       156.23       154.36 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       15.48        14.17        29.85        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 
       37.38         7.50        44.42        38.89         0.56        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93       134.27        95.57       130.78 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL 
       14.30        29.13        93.21         3.65        19.46        16.18 
TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       21.30        75.02        51.88        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 
       36.82       146.14        13.08        73.48        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        18.44        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        28.34        13.68        16.01 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       22.26        28.54        10.78        36.66        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03        16.54         3.75         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
        0.10        37.87        33.01         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 
       27.35         0.10         5.33         2.70        16.93        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L 
       16.83        17.52        17.65         2.43        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       56.58        45.44        41.49        68.32        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       40.01        24.92        31.63        12.76        28.87        20.71 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        14.40        14.40         0.23         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.37         9.44         5.88         7.96         7.59         1.28 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23        13.41         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.70        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        28.37        27.16       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN 
       21.37        19.69        15.98         2.04        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE 
       31.20        30.05        26.14        33.93        26.99        31.36 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       43.20        13.51         0.10         7.89        39.16        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       43.96        43.40        46.88        37.71 

  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                        145.05                         211.17 
  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE 
                         25.15                          22.16 
[1] "0.1 - 145.1 (25.1)" "0.0 - 211.2 (22.2)"
[1] "hr=" "1.7"
D19V2, continuous
D19V3, binary
                                cls
clus                               0   1
  AMP PEAK 19(XP11.22) MUTATED    20  28
  AMP PEAK 19(XP11.22) WILD-TYPE 208 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(XP11.22) MUTATED     20   28
  AMP PEAK 19(XP11.22) WILD-TYPE  208  256
        clus
vv       AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE
  FEMALE                           20                            208
  MALE                             28                            256
[1] 2 2
[1] FALSE
D19V4, binary
                                cls
clus                               0   1
  AMP PEAK 19(XP11.22) MUTATED     7  38
  AMP PEAK 19(XP11.22) WILD-TYPE 177 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(XP11.22) MUTATED      7   38
  AMP PEAK 19(XP11.22) WILD-TYPE  177  257
     clus
vv    AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE
  NO                             7                            177
  YES                           38                            257
[1] 2 2
[1] FALSE
D19V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 19(XP11.22) MUTATED            28               12                 8
  AMP PEAK 19(XP11.22) WILD-TYPE         166              117               181
D19V6, multiclass
                   clus
vv                  AMP PEAK 19(XP11.22) MUTATED AMP PEAK 19(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 28                            166
  OLIGOASTROCYTOMA                            12                            117
  OLIGODENDROGLIOMA                            8                            181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(XP11.22) MUTATED                                  0     2
  AMP PEAK 19(XP11.22) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(XP11.22) MUTATED                           1    45
  AMP PEAK 19(XP11.22) WILD-TYPE                        20   427
D19V7, multiclass
                                  clus
vv                                 AMP PEAK 19(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      45
                                  clus
vv                                 AMP PEAK 19(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       427
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(XP11.22) MUTATED     5  38
  AMP PEAK 19(XP11.22) WILD-TYPE  27 408
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(XP11.22) MUTATED      5   38
  AMP PEAK 19(XP11.22) WILD-TYPE   27  408
                        clus
vv                       AMP PEAK 19(XP11.22) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       AMP PEAK 19(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 27
  NOT HISPANIC OR LATINO                            408
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(XP11.22) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(XP11.22) MUTATED    50  13
  AMP PEAK 20(XP11.22) WILD-TYPE 333 112
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            63                            445 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            13                            112 
$`AMP PEAK 20(XP11.22) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-FG-A713 TCGA-CS-4938 TCGA-CS-6667 TCGA-DB-5277 
       51.55        42.05        20.45       117.50        48.30        50.86 
TCGA-DB-5281 TCGA-DB-A75L TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6401 TCGA-DU-6407 
       78.28        11.24        18.94        75.16        87.45        94.52 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-8167 TCGA-DU-A5TP 
        2.40        62.96        14.99       117.40        15.48        33.27 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5307 TCGA-E1-5318 
       31.69        24.43        26.17        50.14        57.93        78.21 
TCGA-E1-A7YK TCGA-E1-A7Z4 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MY TCGA-HT-7476 
       12.43       145.05        17.88        14.24        23.70         6.54 
TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7857 
       24.26        45.99        31.69        14.96        19.23         0.23 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-A616 TCGA-HT-A618 
       31.43        63.55        12.23         0.10         1.81        16.83 
TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ TCGA-P5-A72W 
       10.52         0.10        69.27        42.54         2.30        10.42 
TCGA-P5-A733 TCGA-QH-A6CV TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-S9-A89V TCGA-TM-A84Q 
       13.61        14.53        19.99        18.54        18.71        25.38 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-VM-A8CF TCGA-WY-A858 
       40.41        44.09        61.41        45.93        20.02        43.96 
TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       39.88        45.80        20.81 

$`AMP PEAK 20(XP11.22) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O TCGA-E1-A7YN 
       46.88        46.72        31.82        62.01        17.16        23.90 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 
       20.09        17.82        18.64        21.40        45.60        42.77 
TCGA-R8-A73M TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
       59.38         7.69        43.89        36.36        60.10        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.26        21.01        53.62         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        46.95        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       12.10        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       46.06        24.59        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        23.21        17.46        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 
       49.02        46.06        65.75         1.22         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
      133.74        19.89        16.83       114.08         7.96        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23       154.36       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       16.96        14.17        29.85        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42        38.89         0.56        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
       79.99       134.27        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO 
       93.21         3.65        19.46        16.18        21.30        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       13.08        73.48        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       42.54        41.33        18.44        15.35        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       20.09        28.34        13.68        16.01        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       32.61        38.27        10.72        18.38        18.71        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       21.53        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       36.66        48.69         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       17.42         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29         3.16        22.06        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        6.05        42.74         0.10         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 
       17.52         6.90        14.53        39.48        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        9.40         0.10        37.87        33.01         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L 
       16.14        17.52        17.65         2.43        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       56.58        45.44        41.49        68.32        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       40.01        24.92        31.63        12.76        28.87        20.71 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        14.40        14.40         0.23         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.37         9.44         5.88         7.96         7.59         1.28 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 
        0.23        13.25        11.64        10.95         9.01         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        13.61        12.23        13.41         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50        16.70 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
        2.04        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA 
       25.87        33.93        26.99        31.36        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        39.16        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A85A TCGA-WY-A85C 
       23.21         8.05        51.06        13.32        43.40        46.88 
TCGA-WY-A85D 
       37.71 

  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                        145.05                         211.17 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                         25.38                          21.57 
[1] "0.1 - 145.1 (25.4)" "0.0 - 211.2 (21.6)"
[1] "hr=" "1.4"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    32  31
  AMP PEAK 20(XP11.22) WILD-TYPE 196 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     32   31
  AMP PEAK 20(XP11.22) WILD-TYPE  196  253
        clus
vv       AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  FEMALE                           32                            196
  MALE                             31                            253
[1] 2 2
[1] FALSE
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    11  48
  AMP PEAK 20(XP11.22) WILD-TYPE 173 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     11   48
  AMP PEAK 20(XP11.22) WILD-TYPE  173  247
     clus
vv    AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  NO                            11                            173
  YES                           48                            247
[1] 2 2
[1] FALSE
D20V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 20(XP11.22) MUTATED            39               15                 9
  AMP PEAK 20(XP11.22) WILD-TYPE         155              114               180
D20V6, multiclass
                   clus
vv                  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 39                            155
  OLIGOASTROCYTOMA                            15                            114
  OLIGODENDROGLIOMA                            9                            180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(XP11.22) MUTATED                                  0     1
  AMP PEAK 20(XP11.22) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(XP11.22) MUTATED                           1    61
  AMP PEAK 20(XP11.22) WILD-TYPE                        20   411
D20V7, multiclass
                                  clus
vv                                 AMP PEAK 20(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      61
                                  clus
vv                                 AMP PEAK 20(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       411
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED     5  52
  AMP PEAK 20(XP11.22) WILD-TYPE  27 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED      5   52
  AMP PEAK 20(XP11.22) WILD-TYPE   27  394
                        clus
vv                       AMP PEAK 20(XP11.22) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK 20(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 27
  NOT HISPANIC OR LATINO                            394
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED   165  38
  DEL PEAK  1(1P36.32) WILD-TYPE 218  87
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           203                            305 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            38                             87 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-CS-6670 TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 
       46.88        31.82        62.01        20.09        17.82        20.45 
TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 
       21.40        42.77        59.38         0.26        53.62        49.94 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG 
       75.25        47.93        91.13        44.52        18.84        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A669 
       27.81        29.23        14.40        12.10        24.59        30.21 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5870 
       17.19        54.25        23.21        14.56         6.74       182.33 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6405 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 
        1.22         7.04        19.89         7.96        11.47       154.36 
TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8158 
      117.40        30.67        10.36        94.32        60.30         5.10 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       21.40        15.48        14.17        25.55        21.57        95.11 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TG TCGA-E1-5311 TCGA-E1-5318 
       22.29        21.30        17.98        44.42       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YY 
       95.57        19.46        21.30        75.02        15.32       146.14 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6692 TCGA-FG-7634 
       39.48         0.23        47.77        52.21        18.44        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-A6IZ 
       22.55        20.61        14.24        16.01        22.52        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7477 
       16.44        36.66         0.10         6.67         0.13        24.26 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 
       75.19        95.93         4.57         3.16        22.06         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 
       14.27        16.24        44.68         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       14.53        39.09         0.23        37.15         0.33         0.13 
TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 
       35.47         1.64         9.40         6.25         5.56        29.59 
TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A61C 
       26.04         0.07        27.35        16.93        16.14        17.65 
TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
        2.43        15.35        11.05        56.58        45.44        68.32 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 
       35.44        24.92        31.63        14.40         7.99         9.44 
TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A737 TCGA-P5-A77W 
        7.59        11.64        10.95         9.01        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        3.45         4.41        15.16        12.62        15.85        14.04 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.83        14.53        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.73        16.70        11.08        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TW 
       30.87         5.46        28.08        30.67        62.17        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       40.93        35.38        29.85        32.61       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
      135.22        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.64        14.07        36.13        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G 
       20.68        28.37        27.16       169.84        49.32        40.64 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI 
       24.79        33.24        18.61        14.93        19.69         2.04 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CA TCGA-VM-A8CB 
       33.73        31.20        26.14        33.93        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
        7.89        39.16        37.05        23.21        51.06 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-A87N 
       51.55        46.72        42.05        17.16        23.90        18.64 
TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       45.60       117.50         7.69        43.89        36.36        60.10 
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       40.18        21.01         6.38        17.69        26.76        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 
       46.95        48.30        49.12       122.73        81.96        72.92 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD 
       50.86        36.56        78.28        46.42        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M 
       37.45        33.57        27.45        18.51        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66D 
       30.74        16.18        19.96        63.88        46.06        27.81 
TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 
       17.19        17.46        13.71        18.61        18.02        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6395 
       13.38         8.45         6.81        18.94       211.17        49.02 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 
       65.75        87.45        11.64       133.74        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 
      114.08         2.40        62.96       156.23        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 
        6.54         8.84        90.77        26.30         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       44.02        25.91        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A5TR 
       14.60        20.68        19.13        16.96        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       31.69        24.43        26.17        24.99        33.96        20.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       11.41        26.76       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        38.89         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       79.99        57.93       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV 
        3.65        12.43        16.18        51.88         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 
       36.82        13.08        73.48       145.05        32.35         0.20 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 
       17.88        20.09        28.34        13.68        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q 
       21.53        22.26        28.54        10.78        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       27.52        11.54        40.11         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 
       17.42         6.54         6.38        40.34       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 
        4.01         5.03        29.85        23.18       122.47        17.29 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 
       45.99        56.09        57.60         0.16         0.76         6.05 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       42.74        31.69        14.96         0.10         0.10        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 
       39.48        19.23        50.63         0.49        23.61         3.68 
TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 
        5.33         3.72        11.28        31.43        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        2.50        13.78         0.23        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.23         0.13        20.22         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 
        1.81        16.83        17.52        10.52         0.10        41.49 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       69.27        39.75        40.01        42.54        12.76        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       20.71        19.00        14.40         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         5.88         7.96         1.28         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S 
       13.25        13.61         9.60         7.56         2.37         2.53 
TCGA-QH-A6CS TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       19.33        13.61        12.23        10.29         1.91        16.50 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TV 
       12.99         9.90         2.07        19.59        87.12        18.77 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       36.82        24.39        25.81        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ 
        5.85        85.55        18.61         7.92        26.93        19.99 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       20.02        15.06        18.54        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        20.48        54.77        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       34.78        65.39        24.92        16.18        59.05        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF 
       28.08        24.16        40.83        25.38        23.80        21.37 
TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-TQ-A7RR 
       15.98        40.41        44.09        36.69        30.05        25.87 
TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CF 
       61.41        26.99        31.36        45.93        43.20        20.02 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.47        16.01         8.05        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        182.33                         211.17 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         21.57                          23.47 
[1] "0.1 - 182.3 (21.6)" "0.0 - 211.2 (23.5)"
[1] "hr=" "1.5"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    95 111
  DEL PEAK  1(1P36.32) WILD-TYPE 133 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     95  111
  DEL PEAK  1(1P36.32) WILD-TYPE  133  173
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           95                            133
  MALE                            111                            173
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    97  97
  DEL PEAK  1(1P36.32) WILD-TYPE  87 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     97   97
  DEL PEAK  1(1P36.32) WILD-TYPE   87  198
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            97                             87
  YES                           97                            198
[1] 2 2
[1] FALSE
D21V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  1(1P36.32) MUTATED            22               46               138
  DEL PEAK  1(1P36.32) WILD-TYPE         172               83                51
D21V6, multiclass
                   clus
vv                  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  ASTROCYTOMA                                 22                            172
  OLIGOASTROCYTOMA                            46                             83
  OLIGODENDROGLIOMA                          138                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.32) MUTATED                                  1     5
  DEL PEAK  1(1P36.32) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED                           7   187
  DEL PEAK  1(1P36.32) WILD-TYPE                        14   285
D21V7, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                     187
                                  clus
vv                                 DEL PEAK  1(1P36.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    13 181
  DEL PEAK  1(1P36.32) WILD-TYPE  19 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     13  181
  DEL PEAK  1(1P36.32) WILD-TYPE   19  265
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          181
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            265
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  2(1P32.3) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P32.3) MUTATED   160  33
  DEL PEAK  2(1P32.3) WILD-TYPE 223  92
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          193                           315 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           33                            92 
$`DEL PEAK  2(1P32.3) MUTATED`
TCGA-CS-6670 TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 
       46.88        31.82        62.01        20.09        17.82        20.45 
TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 
       21.40        42.77        59.38         0.26        53.62        49.94 
TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       75.25        91.13        44.52        18.84        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       24.20        25.48        30.12         5.98        31.40        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       29.23        14.40        12.10        24.59        30.21        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       54.25        23.21        14.56       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 
       22.42        46.06         1.22         7.96       154.36       117.40 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8164 
       30.67        94.32        60.30         5.10        23.74        21.40 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
       15.48        14.17        25.55        21.57        95.11        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TG TCGA-E1-5311 
       11.41        26.76        21.30        17.98        44.42       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YL TCGA-E1-A7YO 
       78.21        95.57       130.78        14.30        16.18        75.02 
TCGA-E1-A7YS TCGA-E1-A7YY TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 
       15.32       146.14        39.48         0.23        47.77        52.21 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8189 
       15.35        22.55        20.61        14.24        16.01        22.52 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 
       15.02        16.44        36.66         5.72         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
        0.13        75.19        95.93         4.57         3.16        22.06 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 
        0.23        14.27        16.24        44.68         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 
        6.90        14.53        39.09         0.23         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 
        0.33         0.13        35.47         1.64         9.40         6.25 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R9 
        5.56        13.78        29.59         0.23        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L 
       16.93        16.14        17.65         2.43        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ 
       56.58        45.44        68.32        35.44        24.92        31.63 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A737 
       14.40         7.99         9.44        11.64        10.95        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
       19.20         3.45         4.41        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        14.83        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       16.73        11.08        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
        5.46        28.08        30.67        41.10        40.93        35.38 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       29.85        32.61       123.65        75.25       135.22        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       84.99        31.10        26.47        18.64        14.07        36.13 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
       23.51         8.19         2.04        20.68        28.37        27.16 
TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R 
      169.84        49.32        40.64        24.79        33.24        18.61 
TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ 
       14.93        19.69         2.04        33.73        31.20        26.14 
TCGA-TQ-A7RU TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
       33.93        13.51         0.10        39.16        37.05        23.21 
TCGA-W9-A837 
       51.06 

$`DEL PEAK  2(1P32.3) WILD-TYPE`
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-A87N 
       51.55        46.72        42.05        17.16        23.90        18.64 
TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       45.60       117.50         7.69        43.89        36.36        60.10 
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       40.18        21.01         6.38        17.69        26.76        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
       46.95        48.30        49.12       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        50.86        36.56        78.28        46.42        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L 
       39.78        37.45        33.57        27.45        18.51        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        63.88        46.06 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       27.81        17.19        17.46        13.71        18.61        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 
       17.46         6.74        13.38         8.45         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 
       17.49       211.17        49.02        75.16        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
      114.08         2.40        11.47        62.96       156.23        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54         8.84        90.77        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
        7.96        18.94        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TP 
        2.76        14.60        20.68        19.13        16.96        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       20.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK 
       57.93        29.13        93.21         3.65        19.46        12.43 
TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z2 
       21.30        51.88         0.76        32.45        36.82        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 
       73.48       145.05        32.35         0.20        25.48        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        42.54        41.33        18.44        17.88 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       20.09        28.34        13.68        14.96        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        14.76        21.53 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7469 
       22.26        28.54        10.78        48.69        27.52        11.54 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       24.26         6.38        40.34       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 
        5.03        29.85        23.18       122.47        17.29        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       56.09        57.60         0.16         0.76         6.05        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 
       31.69        14.96         0.10         0.10        17.52        39.48 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 
       19.23        50.63        23.61         3.68         5.33         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43        16.24        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8111 
       33.01        12.23         0.10         0.46         2.50         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA 
       34.19        28.27        15.72         0.13        20.22        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         5.33         2.70         1.81        16.83        17.52 
TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
       10.52         0.10        41.49        69.27        39.75        40.01 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 
       42.54        12.76        28.87        20.71        19.00        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         2.37         2.30         5.88         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 
        7.59         1.28         0.23        10.42        13.25         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CS 
       13.61         9.60         7.56         2.37         2.53        19.33 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       14.53        13.61        12.23        10.29         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS 
       16.70        12.99         9.90         2.07        19.59        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 
       87.12        18.77        36.82        24.39        25.81        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO 
       98.24        95.93         5.85        85.55        19.86        18.61 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
        7.92        26.93        19.99        20.02        15.06        18.54 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       20.48        54.77        48.33        34.78        65.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        30.44        28.08        24.16        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       25.38        23.80        21.37        15.98        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       36.69        30.05        25.87        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M 
       45.93        43.20         7.89        20.02        23.47        16.01 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       182.33                        211.17 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                        22.42                         22.26 
[1] "0.1 - 182.3 (22.4)" "0.0 - 211.2 (22.3)"
[1] "hr=" "1.8"
D22V2, continuous
D22V3, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    89 107
  DEL PEAK  2(1P32.3) WILD-TYPE 139 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     89  107
  DEL PEAK  2(1P32.3) WILD-TYPE  139  177
        clus
vv       DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  FEMALE                          89                           139
  MALE                           107                           177
[1] 2 2
[1] FALSE
D22V4, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    95  86
  DEL PEAK  2(1P32.3) WILD-TYPE  89 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     95   86
  DEL PEAK  2(1P32.3) WILD-TYPE   89  209
     clus
vv    DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  NO                           95                            89
  YES                          86                           209
[1] 2 2
[1] FALSE
D22V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  2(1P32.3) MUTATED            16               42               138
  DEL PEAK  2(1P32.3) WILD-TYPE         178               87                51
D22V6, multiclass
                   clus
vv                  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  ASTROCYTOMA                                16                           178
  OLIGOASTROCYTOMA                           42                            87
  OLIGODENDROGLIOMA                         138                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P32.3) MUTATED                                  1     4
  DEL PEAK  2(1P32.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P32.3) MUTATED                           6   179
  DEL PEAK  2(1P32.3) WILD-TYPE                        15   293
D22V7, multiclass
                                  clus
vv                                 DEL PEAK  2(1P32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                    179
                                  clus
vv                                 DEL PEAK  2(1P32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    13 172
  DEL PEAK  2(1P32.3) WILD-TYPE  19 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     13  172
  DEL PEAK  2(1P32.3) WILD-TYPE   19  274
                        clus
vv                       DEL PEAK  2(1P32.3) MUTATED
  HISPANIC OR LATINO                              13
  NOT HISPANIC OR LATINO                         172
                        clus
vv                       DEL PEAK  2(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D23V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    23  12
  DEL PEAK  3(1Q43) WILD-TYPE 360 113
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         35                         473 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         12                         113 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-HT-A619 TCGA-DU-5852 TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7015 
       21.40         6.74        18.94        75.16         2.40        90.77 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A5TS TCGA-DU-A76K TCGA-DU-A7TA TCGA-DU-A7TG 
        5.10        23.74        31.69        11.41        84.33        44.42 
TCGA-E1-5302 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YY TCGA-FG-8185 TCGA-FG-A6J3 
       50.14       130.78        32.45       146.14        14.24        22.26 
TCGA-HT-7477 TCGA-HT-7485 TCGA-HT-7857 TCGA-HT-8109 TCGA-HT-8113 TCGA-P5-A5F4 
       24.26         4.01         0.23         5.56        29.59         7.59 
TCGA-P5-A72U TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CW TCGA-S9-A6WI TCGA-S9-A7R1 
        0.23         2.37         2.53        13.61        84.99       169.84 
TCGA-S9-A89Z TCGA-TM-A84I TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RW 
       20.48        28.08        23.80        21.37        26.99 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       36.36        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        6.38        17.69        26.76        37.38        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.94        49.12       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        91.13        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       63.88        46.06        24.59        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        23.21        17.46        13.71        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        14.56        17.46        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96        11.47        62.96       156.23       154.36        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        33.27 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       29.85        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R 
       21.57        95.11        20.98        22.29        26.76        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TI 
       17.98       139.04        51.52        37.38         7.50        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
       78.21        95.57        14.30        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        12.43        16.18        21.30        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       15.32         0.76        36.82        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       28.34        13.68        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       48.69         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
      172.77         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
        0.46         2.50        13.78         0.23        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       24.92        31.63        12.76        28.87        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72W 
        2.30         9.44         5.88         7.96         1.28        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 
       13.25        11.64        10.95         9.01        13.61         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        7.56        12.23        19.20         3.45         4.41        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       27.16        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71        54.77        48.33        49.32        34.78        65.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       61.41        31.36        45.93        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        7.89        39.16        20.02        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.23                        0.03 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     169.84                      211.17 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      22.26                       22.42 
[1] "0.2 - 169.8 (22.3)" "0.0 - 211.2 (22.4)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    19  16
  DEL PEAK  3(1Q43) WILD-TYPE 209 268
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     19   16
  DEL PEAK  3(1Q43) WILD-TYPE  209  268
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        19                         209
  MALE                          16                         268
[1] 2 2
[1] FALSE
D23V4, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    10  23
  DEL PEAK  3(1Q43) WILD-TYPE 174 272
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     10   23
  DEL PEAK  3(1Q43) WILD-TYPE  174  272
     clus
vv    DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  NO                         10                         174
  YES                        23                         272
[1] 2 2
[1] FALSE
D23V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  3(1Q43) MUTATED            10               11                14
  DEL PEAK  3(1Q43) WILD-TYPE         184              118               175
D23V6, multiclass
                   clus
vv                  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  ASTROCYTOMA                              10                         184
  OLIGOASTROCYTOMA                         11                         118
  OLIGODENDROGLIOMA                        14                         175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q43) MUTATED                                  0     1
  DEL PEAK  3(1Q43) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED                           2    32
  DEL PEAK  3(1Q43) WILD-TYPE                        19   440
D23V7, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   32
                                  clus
vv                                 DEL PEAK  3(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     2  33
  DEL PEAK  3(1Q43) WILD-TYPE  30 413
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      2   33
  DEL PEAK  3(1Q43) WILD-TYPE   30  413
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             2                          30
  NOT HISPANIC OR LATINO                        33                         413
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    53  23
  DEL PEAK  4(2Q37.3) WILD-TYPE 330 102
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           76                           432 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           23                           102 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-DH-A66B TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5270 TCGA-DB-5277 
       42.05        36.36         6.38        46.95       122.73        50.86 
TCGA-DB-5281 TCGA-DB-A64P TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-5855 
       78.28        30.12        63.88        30.21        54.25         6.81 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 
       49.02        75.16        94.52       114.08         2.40        62.96 
TCGA-DU-7008 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8167 TCGA-DU-A5TR 
      156.23       117.40        23.31        41.98        15.48        29.85 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-DU-A7TI TCGA-E1-5304 
       31.69        24.99        20.98        17.98        38.89        41.13 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YM TCGA-F6-A8O4 TCGA-FG-A6J3 
       29.13        93.21        12.43        21.30         0.20        22.26 
TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-7692 
       16.54        24.26         5.03        17.29         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-8013 TCGA-HT-A5RB TCGA-HT-A618 TCGA-HT-A61B 
       17.52        19.23        63.55         0.10        16.83        17.52 
TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5EW TCGA-P5-A5F6 TCGA-P5-A72W 
       69.27        42.54        19.00         6.71         1.28        10.42 
TCGA-P5-A733 TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-RY-A83Z 
       13.61        14.53        13.61        10.29         1.91         9.90 
TCGA-RY-A845 TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WQ TCGA-S9-A7J0 TCGA-S9-A89Z 
       19.59        35.15        85.55        14.07        20.02        20.48 
TCGA-TM-A7CA TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TQ-A7RF 
       34.78        28.08        40.83        33.24        25.38        21.37 
TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RW 
       15.98        44.09        36.69        26.99 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 
       60.10        40.18         0.26        21.01        53.62        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       26.76        37.38        48.30        49.94        49.12        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        24.20        25.48         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        19.96        46.06 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       24.59        27.81        17.19        17.19        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
      211.17        52.11        22.42        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
        7.96        11.47       154.36        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7309 
       94.32        18.94        44.02        25.91        60.30         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       16.96        14.17        33.27        24.43        26.17        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        95.11        22.29        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42         0.56        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YI 
      134.27        78.21        95.57       130.78        14.30         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU 
       19.46        16.18        75.02        51.88        15.32         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       48.69         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.13         0.03         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        4.01        29.85        23.18       122.47         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 
        0.10        31.69        14.96         0.10         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07        27.35         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        1.81        16.14        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        56.58        45.44        41.49        68.32 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       35.44        39.75        40.01        24.92        31.63        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX 
       28.87        20.71        14.40        14.40         0.23         7.99 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         9.44         5.88         7.96         7.59 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 
        0.23        13.25        11.64        10.95         9.01         9.60 
TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        7.56        12.23        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.83        12.23        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.73        16.50        16.70        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       94.03        32.65        30.87         5.46        28.08         2.07 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       31.59        18.71        54.77        48.33        49.32        65.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84M TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RI 
       24.79        18.61        14.93        23.80        19.69         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       40.41        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       33.93        61.41        31.36        45.93        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       24.625                        21.815 
[1] "0.1 - 156.2 (24.6)" "0.0 - 211.2 (21.8)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    31  46
  DEL PEAK  4(2Q37.3) WILD-TYPE 197 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     31   46
  DEL PEAK  4(2Q37.3) WILD-TYPE  197  238
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          31                           197
  MALE                            46                           238
[1] 2 2
[1] FALSE
D24V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    18  53
  DEL PEAK  4(2Q37.3) WILD-TYPE 166 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     18   53
  DEL PEAK  4(2Q37.3) WILD-TYPE  166  242
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           18                           166
  YES                          53                           242
[1] 2 2
[1] FALSE
D24V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  4(2Q37.3) MUTATED            37               23                17
  DEL PEAK  4(2Q37.3) WILD-TYPE         157              106               172
D24V6, multiclass
                   clus
vv                  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  ASTROCYTOMA                                37                           157
  OLIGOASTROCYTOMA                           23                           106
  OLIGODENDROGLIOMA                          17                           172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     2
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           3    72
  DEL PEAK  4(2Q37.3) WILD-TYPE                        18   400
D24V7, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     72
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      400
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     7  69
  DEL PEAK  4(2Q37.3) WILD-TYPE  25 377
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      7   69
  DEL PEAK  4(2Q37.3) WILD-TYPE   25  377
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                25
  NOT HISPANIC OR LATINO                           377
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED    33  15
  DEL PEAK  5(3P21.31) WILD-TYPE 350 110
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            48                            460 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            15                            110 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-DU-7300 TCGA-HT-A619 TCGA-DB-5275 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 
       62.01        21.40        47.93        50.86        27.81        75.16 
TCGA-DU-6542 TCGA-DU-7010 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A76R 
        2.40        14.99        14.17        24.43        26.17        21.30 
TCGA-DU-A7TA TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YQ 
       84.33        41.13       130.78        19.46        12.43        51.88 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-HT-7469 TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7478 
       32.45        36.82        11.54        16.54        24.26         6.38 
TCGA-HT-7482 TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5R7 
      106.95        17.29         0.10         0.23        15.72        20.22 
TCGA-HT-A5RA TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A6X9 
       27.35        19.00         1.28        19.20         2.37         1.91 
TCGA-S9-A6WG TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A89V TCGA-TM-A84H TCGA-TM-A84J 
       85.55        19.99        20.02        18.71        30.44        24.16 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VV-A829 TCGA-WY-A859 TCGA-WY-A85E 
       15.98        26.99        45.93        37.05        39.88        20.81 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        42.05        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 
       23.90        20.09        17.82        20.45        18.64        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
       49.12       122.73        81.96        75.25        72.92        91.13 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       30.21        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.71        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       154.36       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       31.69        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7T8 
       20.98        22.29        11.41        26.76        17.98       139.04 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YL 
       95.57        14.30        29.13        93.21         3.65        16.18 
TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z2 
       21.30        75.02        15.32         0.76       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        28.34        13.68        14.24        16.01 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       22.26        28.54        10.78        36.66        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        40.11         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54        40.34        75.19        95.93 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         5.56        13.78        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB 
       28.27         0.23        26.04         0.13         0.07         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        28.87        20.71        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.96         7.59         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       13.41         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       32.65        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       40.93        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       75.25       135.22        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       26.93        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI 
       18.61        14.93        23.80        21.37        19.69         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C9 
       26.14        25.87        33.93        61.41        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.40        45.80        46.88        37.71 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         21.35                          22.47 
[1] "0.1 - 130.8 (21.4)" "0.0 - 211.2 (22.5)"
[1] "hr=" "1.4"
D25V2, continuous
D25V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    23  26
  DEL PEAK  5(3P21.31) WILD-TYPE 205 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     23   26
  DEL PEAK  5(3P21.31) WILD-TYPE  205  258
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                           23                            205
  MALE                             26                            258
[1] 2 2
[1] FALSE
D25V4, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED     9  38
  DEL PEAK  5(3P21.31) WILD-TYPE 175 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      9   38
  DEL PEAK  5(3P21.31) WILD-TYPE  175  257
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                             9                            175
  YES                           38                            257
[1] 2 2
[1] FALSE
D25V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  5(3P21.31) MUTATED            19               15                15
  DEL PEAK  5(3P21.31) WILD-TYPE         175              114               174
D25V6, multiclass
                   clus
vv                  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  ASTROCYTOMA                                 19                            175
  OLIGOASTROCYTOMA                            15                            114
  OLIGODENDROGLIOMA                           15                            174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P21.31) MUTATED                                  0     1
  DEL PEAK  5(3P21.31) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED                           2    46
  DEL PEAK  5(3P21.31) WILD-TYPE                        19   426
D25V7, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      46
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       426
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED     5  41
  DEL PEAK  5(3P21.31) WILD-TYPE  27 405
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      5   41
  DEL PEAK  5(3P21.31) WILD-TYPE   27  405
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                 27
  NOT HISPANIC OR LATINO                            405
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  6(3Q13.31) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3Q13.31) MUTATED    23  16
  DEL PEAK  6(3Q13.31) WILD-TYPE 360 109
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            39                            469 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            16                            109 
$`DEL PEAK  6(3Q13.31) MUTATED`
TCGA-DU-7300 TCGA-DU-A76O TCGA-HT-A619 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 
       62.01        17.16        21.40        46.95        50.86        78.28 
TCGA-DU-6402 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-8167 TCGA-DU-A5TU 
        7.04         2.40        62.96       117.40        15.48        26.17 
TCGA-DU-A5TW TCGA-DU-A76K TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YH TCGA-E1-A7YQ 
       24.99        11.41        21.30        50.14        93.21        51.88 
TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-HT-7469 TCGA-HT-7603 TCGA-HT-7606 
       32.45        32.35        25.48        11.54        23.18        17.29 
TCGA-HT-8111 TCGA-HT-8564 TCGA-HW-7489 TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5F2 
        0.23        15.72        41.49        42.54        19.00         7.96 
TCGA-P5-A5F6 TCGA-P5-A733 TCGA-P5-A77W TCGA-P5-A780 TCGA-S9-A6TV TCGA-TM-A84J 
        1.28        13.61        19.20         2.37        18.77        24.16 
TCGA-VM-A8C8 TCGA-WY-A85C TCGA-WY-A85E 
       45.93        46.88        20.81 

$`DEL PEAK  6(3Q13.31) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-E1-A7YN 
       51.55        46.88        46.72        31.82        42.05        23.90 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 TCGA-IK-8125 
       20.09        17.82        20.45        18.64        45.60        42.77 
TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       59.38       117.50         7.69        43.89        36.36        60.10 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.26        21.01        53.62         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       26.76        37.38        48.30        49.94        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        91.13        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       19.96        63.88        46.06        24.59        30.21        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        23.21        17.46        13.71 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22        87.45        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 
       16.83        94.52       114.08         7.96        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      154.36        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        14.17        33.27        29.85        31.69        24.43 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       26.76        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42        38.89         0.56        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        29.13         3.65        19.46        12.43        16.18 
TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY 
       21.30        75.02        15.32         0.76        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       13.08        73.48       145.05        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       20.09        28.34        13.68        14.24        16.01        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       23.70        14.76        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 
       28.54        10.78        36.66        48.69         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       29.85       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
       13.78        29.59        34.19        28.27         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       56.58        45.44        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       40.01        24.92        31.63        12.76        28.87        20.71 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        2.30         9.44         5.88         7.59         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 
       13.25        11.64        10.95         9.01         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       12.23         3.45         4.41        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        40.93        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       27.16       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
        2.04        40.41        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       30.05        26.14        25.87        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       31.36        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85D 
       37.71 

  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                          0.23                           0.03 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                        117.40                         211.17 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                         23.18                          22.29 
[1] "0.2 - 117.4 (23.2)" "0.0 - 211.2 (22.3)"
[1] "hr=" "1.9"
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED    16  23
  DEL PEAK  6(3Q13.31) WILD-TYPE 212 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED     16   23
  DEL PEAK  6(3Q13.31) WILD-TYPE  212  261
        clus
vv       DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  FEMALE                           16                            212
  MALE                             23                            261
[1] 2 2
[1] FALSE
D26V4, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED     9  28
  DEL PEAK  6(3Q13.31) WILD-TYPE 175 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED      9   28
  DEL PEAK  6(3Q13.31) WILD-TYPE  175  267
     clus
vv    DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  NO                             9                            175
  YES                           28                            267
[1] 2 2
[1] FALSE
D26V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  6(3Q13.31) MUTATED            18                9                12
  DEL PEAK  6(3Q13.31) WILD-TYPE         176              120               177
D26V6, multiclass
                   clus
vv                  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  ASTROCYTOMA                                 18                            176
  OLIGOASTROCYTOMA                             9                            120
  OLIGODENDROGLIOMA                           12                            177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3Q13.31) MUTATED                                  0     1
  DEL PEAK  6(3Q13.31) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q13.31) MUTATED                           2    36
  DEL PEAK  6(3Q13.31) WILD-TYPE                        19   436
D26V7, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      36
                                  clus
vv                                 DEL PEAK  6(3Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED     2  34
  DEL PEAK  6(3Q13.31) WILD-TYPE  30 412
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED      2   34
  DEL PEAK  6(3Q13.31) WILD-TYPE   30  412
                        clus
vv                       DEL PEAK  6(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK  6(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 30
  NOT HISPANIC OR LATINO                            412
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  7(3Q29) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3Q29) MUTATED    28  19
  DEL PEAK  7(3Q29) WILD-TYPE 355 106
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         47                         461 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         19                         106 
$`DEL PEAK  7(3Q29) MUTATED`
TCGA-DU-7300 TCGA-HT-A619 TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 
       62.01        21.40        37.38        46.95        50.86        78.28 
TCGA-DH-A7UU TCGA-DU-6395 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7298 
       13.71        49.02        62.96        14.99       117.40        18.94 
TCGA-DU-8161 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YI 
       23.74        15.48        26.17        21.30        50.14         3.65 
TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-6691 TCGA-FG-A6J3 
       16.18        51.88        32.45        25.48        41.33        22.26 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7688 TCGA-HT-8111 
       40.11         0.03        24.26       122.47        31.69         0.23 
TCGA-HT-8564 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A733 TCGA-P5-A77W TCGA-P5-A780 
       15.72        19.00         1.28        13.61        19.20         2.37 
TCGA-QH-A65S TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84J 
        2.53        19.99        20.02        20.48        24.92        24.16 
TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-WY-A859 TCGA-WY-A85C 
       44.09        61.41        45.93        39.88        46.88 

$`DEL PEAK  7(3Q29) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        42.05        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 
       23.90        20.09        17.82        20.45        18.64        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       17.69        26.76        48.30        49.94        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        91.13        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       19.96        63.88        46.06        24.59        30.21        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       17.19        17.19        54.25        23.21        17.46        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         2.40        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      154.36       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 
       26.30        10.36         7.96        94.32        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 
       60.30        23.31        41.98         2.76         5.10        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        14.17        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       29.85        31.69        24.43        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42        38.89         0.56        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YO 
       29.13        93.21        19.46        12.43        21.30        75.02 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 
       52.21        36.82        18.77        14.93        42.54        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       48.69         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.13        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
        5.03        29.85        23.18         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        5.56        13.78        29.59        34.19        28.27         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        28.87        20.71        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.96         7.59         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77X 
       10.95         9.01         9.60         7.56        12.23         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        4.41        15.16        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23        13.41         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.70        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       26.93        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.54        28.37        27.16       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        65.39        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
        2.04        40.41        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       26.14        25.87        33.93        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D TCGA-WY-A85E 
       43.96        43.40        45.80        37.71        20.81 

  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                     122.47                      211.17 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                      24.26                       21.57 
[1] "0.0 - 122.5 (24.3)" "0.1 - 211.2 (21.6)"
[1] "hr=" "1.8"
D27V2, continuous
D27V3, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED    20  27
  DEL PEAK  7(3Q29) WILD-TYPE 208 257
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     20   27
  DEL PEAK  7(3Q29) WILD-TYPE  208  257
        clus
vv       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  FEMALE                        20                         208
  MALE                          27                         257
[1] 2 2
[1] FALSE
D27V4, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED    12  33
  DEL PEAK  7(3Q29) WILD-TYPE 172 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     12   33
  DEL PEAK  7(3Q29) WILD-TYPE  172  262
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  NO                         12                         172
  YES                        33                         262
[1] 2 2
[1] FALSE
D27V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  7(3Q29) MUTATED            25                9                13
  DEL PEAK  7(3Q29) WILD-TYPE         169              120               176
D27V6, multiclass
                   clus
vv                  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  ASTROCYTOMA                              25                         169
  OLIGOASTROCYTOMA                          9                         120
  OLIGODENDROGLIOMA                        13                         176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q29) MUTATED                                  0     1
  DEL PEAK  7(3Q29) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q29) MUTATED                           3    42
  DEL PEAK  7(3Q29) WILD-TYPE                        18   430
D27V7, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   42
                                  clus
vv                                 DEL PEAK  7(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    430
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     4  39
  DEL PEAK  7(3Q29) WILD-TYPE  28 407
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      4   39
  DEL PEAK  7(3Q29) WILD-TYPE   28  407
                        clus
vv                       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             4                          28
  NOT HISPANIC OR LATINO                        39                         407
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  8(4Q34.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q34.3) MUTATED   105  31
  DEL PEAK  8(4Q34.3) WILD-TYPE 278  94
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          136                           372 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           31                            94 
$`DEL PEAK  8(4Q34.3) MUTATED`
TCGA-DH-A66B TCGA-FG-A713 TCGA-HT-A619 TCGA-IK-8125 TCGA-CS-4943 TCGA-CS-6666 
       42.05        20.45        21.40        42.77        36.36        46.95 
TCGA-CS-6667 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 
       48.30        75.25        47.93        50.86        44.52        78.28 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A4XH TCGA-DB-A64W TCGA-DB-A75O TCGA-DH-A669 
       18.84        37.45        31.63        14.40        30.74        30.21 
TCGA-DH-A66G TCGA-DH-A7UV TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-5874 
       17.19        18.61        17.46        13.38        18.94        15.16 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 
       65.75         1.22        19.89         7.96        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 
       14.99        30.67        94.32        44.02        25.91        60.30 
TCGA-DU-7309 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
        2.76        19.13        14.17        29.85        31.69        26.17 
TCGA-DU-A5TW TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       24.99        21.57        22.29        21.30       139.04        84.33 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YK TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        14.30        12.43        15.32        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 
        0.20        47.77        25.48        52.21        17.88        22.55 
TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       14.24        14.96        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
       16.44        22.26         0.10         6.67        11.54         0.13 
TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 
       16.54         6.54        24.26        75.19        16.24        31.69 
TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RC 
        2.96        39.09         6.25        20.22         0.07         5.33 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
       10.52        15.35        45.44        41.49        68.32        69.27 
TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A733 TCGA-P5-A735 
       42.54        19.00         0.23         2.30        13.61         9.60 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A6X4 TCGA-QH-A6XA TCGA-RY-A83Z 
       12.23        19.20         2.37        14.53        16.50         9.90 
TCGA-S9-A6TW TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IY 
       41.10        75.25        31.10        18.64         7.92        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       19.99        20.02        28.37        20.48        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RK 
       34.78        65.39        18.61        23.80        21.37        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RO TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-VM-A8C8 
       36.69        31.20        25.87        33.93        26.99        45.93 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       13.32        39.88        43.40        20.81 

$`DEL PEAK  8(4Q34.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A87N TCGA-HW-7490 TCGA-R8-A73M 
       23.90        20.09        17.82        18.64        45.60        59.38 
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 
      117.50         7.69        43.89        60.10        40.18         0.26 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01        53.62         6.38        17.69        26.76        37.38 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 
       49.94        49.12       122.73        81.96        72.92        91.13 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       36.56        46.42        30.21        39.78        33.57        72.95 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        18.51        12.10        11.24        17.88 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       16.18        19.96        63.88        46.06        24.59        27.81 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-5847 
       17.19        54.25        23.21        17.46        13.71        18.02 
TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
       14.56         6.74         8.45         6.81       182.33        17.49 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04        11.64       133.74        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
      114.08         2.40        11.47       154.36       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       18.94        23.31        41.98         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT 
       20.68        21.40        16.96        15.48        33.27        24.43 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L 
       33.96        25.55        95.11        20.98        11.41        26.76 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       17.98        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI 
        0.56        78.21        95.57        29.13        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU 
       19.46        16.18        21.30        75.02        51.88         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       32.45        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       32.35        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       18.44        15.35        20.61        20.09        28.34        13.68 
TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       18.71        28.54        10.78        36.66        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 
       27.52        40.11         0.03         3.75        17.42         6.38 
TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       40.34        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
        0.16         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        37.87        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74L TCGA-HT-A74O 
       16.83        17.52        17.65         2.43        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       56.58        35.44        39.75        40.01        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW 
       12.76        28.87        20.71        14.40        14.40         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        7.99         2.37         9.44         5.88         7.96         7.59 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.23        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A736 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
        9.01         7.56         3.45         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 
       13.61        12.23        13.41         9.17        10.29        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.73         1.91        16.70        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       94.03        32.65        30.87         5.46        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        18.77        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE 
       35.15        98.24        95.93         5.85       123.65       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        19.86        26.47        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       14.07        36.13        26.93         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        18.54        27.16       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B 
       30.05        98.63        31.59        18.71        54.77        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TQ-A7RG 
       40.83        24.79        33.24        25.38        14.93        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RN TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       15.98         2.04        40.41        33.73        30.05        26.14 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       61.41        31.36        43.20        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
       39.16        20.02        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
        8.05        51.06        43.96        45.80        46.88        37.71 

  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                        23.03                         21.73 
[1] "0.1 - 156.2 (23.0)" "0.0 - 211.2 (21.7)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED    57  80
  DEL PEAK  8(4Q34.3) WILD-TYPE 171 204
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     57   80
  DEL PEAK  8(4Q34.3) WILD-TYPE  171  204
        clus
vv       DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  FEMALE                          57                           171
  MALE                            80                           204
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED    45  82
  DEL PEAK  8(4Q34.3) WILD-TYPE 139 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     45   82
  DEL PEAK  8(4Q34.3) WILD-TYPE  139  213
     clus
vv    DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  NO                           45                           139
  YES                          82                           213
[1] 2 2
[1] FALSE
D28V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  8(4Q34.3) MUTATED            48               36                53
  DEL PEAK  8(4Q34.3) WILD-TYPE         146               93               136
D28V6, multiclass
                   clus
vv                  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  ASTROCYTOMA                                48                           146
  OLIGOASTROCYTOMA                           36                            93
  OLIGODENDROGLIOMA                          53                           136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q34.3) MUTATED                                  0     3
  DEL PEAK  8(4Q34.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.3) MUTATED                           4   129
  DEL PEAK  8(4Q34.3) WILD-TYPE                        17   343
D28V7, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                    129
                                  clus
vv                                 DEL PEAK  8(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED    10 119
  DEL PEAK  8(4Q34.3) WILD-TYPE  22 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     10  119
  DEL PEAK  8(4Q34.3) WILD-TYPE   22  327
                        clus
vv                       DEL PEAK  8(4Q34.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       DEL PEAK  8(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                22
  NOT HISPANIC OR LATINO                           327
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  9(5P15.33) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(5P15.33) MUTATED    36  14
  DEL PEAK  9(5P15.33) WILD-TYPE 347 111
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            50                            458 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            14                            111 
$`DEL PEAK  9(5P15.33) MUTATED`
TCGA-DB-A4XC TCGA-E1-A7YN TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5281 
       46.72        23.90        36.36        47.93        72.92        78.28 
TCGA-DB-A4XE TCGA-DB-A4XH TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G 
       37.45        31.63        18.51        19.96        27.81        17.19 
TCGA-DU-6399 TCGA-DU-7007 TCGA-DU-7306 TCGA-DU-8165 TCGA-DU-A7T6 TCGA-E1-5302 
       65.75        62.96        41.98        19.13        17.98        50.14 
TCGA-E1-5304 TCGA-E1-A7YI TCGA-E1-A7YV TCGA-E1-A7Z4 TCGA-FG-5962 TCGA-FG-5965 
       41.13         3.65        32.45       145.05        47.77        36.82 
TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-HT-7474 TCGA-HT-7475 
       14.93        18.38        23.70        22.26         3.75        17.42 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8106 
       31.69        14.96        23.61         3.68        11.28         0.10 
TCGA-HT-A614 TCGA-HT-A61B TCGA-HT-A74O TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A780 
        2.70        17.52         0.10         7.59        10.42         2.37 
TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R7 TCGA-TM-A84I 
        9.90        18.77        19.86        26.93        98.63        28.08 
TCGA-TQ-A7RH TCGA-WY-A859 
       15.98        39.88 

$`DEL PEAK  9(5P15.33) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        31.82        42.05        62.01        17.16 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 
       20.09        17.82        20.45        18.64        21.40        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 
       42.77        59.38       117.50         7.69        43.89        60.10 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.26        21.01        53.62         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       26.76        37.38        46.95        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
      122.73        81.96        75.25        50.86        91.13        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF 
       36.56        46.42        18.84        30.21        39.78        33.57 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        16.18        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       30.21        17.19        54.25        23.21        17.46        13.71 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         2.40        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       95.11        20.98        22.29        11.41        26.76        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       38.89         0.56        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        12.43        16.18        21.30        75.02        51.88 
TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       15.32         0.76        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        25.48        52.21 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        42.54        41.33        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y 
       18.71        14.76        21.53        15.02        16.44        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       10.78        36.66        48.69         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 
        0.33         0.13         5.33        35.47         3.72        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         5.33        16.93         1.81        16.14        16.83 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.65         2.43        10.52        15.35        11.05        56.58 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       45.44        41.49        68.32        69.27        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54        24.92        31.63        12.76        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        14.40        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        7.99         2.37         2.30         9.44         5.88         7.96 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.23        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       32.65        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        62.17        87.12        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       85.55        38.56        84.99        31.10        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        14.07        36.13         7.92        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        27.16       169.84        10.39        99.06        30.05 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI 
       18.61        14.93        23.80        21.37        19.69         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       45.93        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       51.06        13.32        43.96        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                        145.05                         211.17 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                        22.935                         22.355 
[1] "0.1 - 145.1 (22.9)" "0.0 - 211.2 (22.4)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED    21  29
  DEL PEAK  9(5P15.33) WILD-TYPE 207 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED     21   29
  DEL PEAK  9(5P15.33) WILD-TYPE  207  255
        clus
vv       DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           21                            207
  MALE                             29                            255
[1] 2 2
[1] FALSE
D29V4, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED     6  40
  DEL PEAK  9(5P15.33) WILD-TYPE 178 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED      6   40
  DEL PEAK  9(5P15.33) WILD-TYPE  178  255
     clus
vv    DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  NO                             6                            178
  YES                           40                            255
[1] 2 2
[1] FALSE
D29V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  9(5P15.33) MUTATED            23               19                 8
  DEL PEAK  9(5P15.33) WILD-TYPE         171              110               181
D29V6, multiclass
                   clus
vv                  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  ASTROCYTOMA                                 23                            171
  OLIGOASTROCYTOMA                            19                            110
  OLIGODENDROGLIOMA                            8                            181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(5P15.33) MUTATED                                  0     0
  DEL PEAK  9(5P15.33) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5P15.33) MUTATED                           1    49
  DEL PEAK  9(5P15.33) WILD-TYPE                        20   423
D29V7, multiclass
                                  clus
vv                                 DEL PEAK  9(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      49
                                  clus
vv                                 DEL PEAK  9(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       423
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED     2  46
  DEL PEAK  9(5P15.33) WILD-TYPE  30 400
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED      2   46
  DEL PEAK  9(5P15.33) WILD-TYPE   30  400
                        clus
vv                       DEL PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       DEL PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 30
  NOT HISPANIC OR LATINO                            400
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 10(5Q34) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(5Q34) MUTATED    44  20
  DEL PEAK 10(5Q34) WILD-TYPE 339 105
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         64                         444 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         20                         105 
$`DEL PEAK 10(5Q34) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-CS-6666 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 
       51.55        42.05        46.95        72.92        50.86        78.28 
TCGA-DB-A4XH TCGA-DB-A64X TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G 
       31.63        18.51        11.24        19.96        27.81        17.19 
TCGA-DH-A7UU TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7010 
       13.71        65.75        87.45       114.08        62.96        14.99 
TCGA-DU-8165 TCGA-DU-A5TU TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5304 
       19.13        26.17        20.98        17.98        50.14        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YE TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-A6J3 
       79.99        57.93        29.13        25.48        17.88        22.26 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7879 TCGA-HT-7884 
       11.54        40.11        24.26        45.99         3.68        11.28 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A618 TCGA-HW-7489 
       31.43         0.10        20.22         2.70        16.83        41.49 
TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-QH-A65S TCGA-RY-A83Z 
       19.00         2.30         5.88        13.25         2.53         9.90 
TCGA-S9-A6TS TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IS 
       62.17        18.77        19.86        18.61        18.64         7.92 
TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84I TCGA-TQ-A7RM TCGA-VM-A8CF 
       98.63        20.48        65.39        28.08        36.69        20.02 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85D 
       13.32        39.88        45.80        37.71 

$`DEL PEAK 10(5Q34) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O TCGA-E1-A7YN 
       46.88        46.72        31.82        62.01        17.16        23.90 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 
       20.09        17.82        20.45        18.64        21.40        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        26.76        37.38        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 
      122.73        81.96        75.25        47.93        91.13        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        16.18        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       30.21        17.19        54.25        23.21        17.46        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       52.11        22.42        49.02        75.16        46.06         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.96         2.40        11.47       156.23       154.36       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       33.27        29.85        31.69        24.43        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        95.11        22.29        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 
       44.42        38.89         0.56        67.46       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ 
       95.57       130.78        14.30        93.21         3.65        19.46 
TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       12.43        16.18        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
        0.76        32.45        36.82       146.14        13.08        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       52.21        36.82        18.77        14.93        42.54        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        15.35        22.55        20.61        20.09        28.34 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       21.53        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 
       48.69         5.72        27.52         0.10         6.67         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 
        0.13         5.33        35.47         3.72         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
        0.13         0.07        27.35         0.10         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.14        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
       15.35        11.05         0.10        56.58        45.44        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54        24.92 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 
       31.63        12.76        28.87        20.71        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 
        0.23         6.71         7.99         2.37         9.44         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 
        7.59         1.28         0.23        10.42        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        3.45         2.37         4.41        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       13.41         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50        16.70        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       94.03        32.65        30.87         5.46        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       19.59        30.67        87.12        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WQ 
       85.55        38.56        84.99        31.10        26.47        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V 
      169.84        10.39        99.06        30.05        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C 
       54.77        48.33        49.32        34.78        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        30.44        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN 
       19.69        15.98         2.04        40.41        44.09        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV 
       31.20        30.05        26.14        25.87        33.93        61.41 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       26.99        31.36        45.93        43.20        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        39.16        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85E 
        8.05        51.06        43.96        43.40        46.88        20.81 

  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                     114.08                      211.17 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                     23.260                      22.355 
[1] "0.1 - 114.1 (23.3)" "0.0 - 211.2 (22.4)"
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED    30  34
  DEL PEAK 10(5Q34) WILD-TYPE 198 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED     30   34
  DEL PEAK 10(5Q34) WILD-TYPE  198  250
        clus
vv       DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  FEMALE                        30                         198
  MALE                          34                         250
[1] 2 2
[1] FALSE
D30V4, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED    11  48
  DEL PEAK 10(5Q34) WILD-TYPE 173 247
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED     11   48
  DEL PEAK 10(5Q34) WILD-TYPE  173  247
     clus
vv    DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  NO                         11                         173
  YES                        48                         247
[1] 2 2
[1] FALSE
D30V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 10(5Q34) MUTATED            41               14                 9
  DEL PEAK 10(5Q34) WILD-TYPE         153              115               180
D30V6, multiclass
                   clus
vv                  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  ASTROCYTOMA                              41                         153
  OLIGOASTROCYTOMA                         14                         115
  OLIGODENDROGLIOMA                         9                         180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q34) MUTATED                                  0     0
  DEL PEAK 10(5Q34) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q34) MUTATED                           0    64
  DEL PEAK 10(5Q34) WILD-TYPE                        21   408
D30V7, multiclass
                                  clus
vv                                 DEL PEAK 10(5Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                   64
                                  clus
vv                                 DEL PEAK 10(5Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                    408
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED     2  58
  DEL PEAK 10(5Q34) WILD-TYPE  30 388
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED      2   58
  DEL PEAK 10(5Q34) WILD-TYPE   30  388
                        clus
vv                       DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  HISPANIC OR LATINO                             2                          30
  NOT HISPANIC OR LATINO                        58                         388
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 11(6P25.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P25.3) MUTATED    28  21
  DEL PEAK 11(6P25.3) WILD-TYPE 355 104
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           49                           459 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           21                           104 
$`DEL PEAK 11(6P25.3) MUTATED`
TCGA-HW-7490 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH 
       45.60         6.38        46.95        50.86        33.57        31.63 
TCGA-DB-A64O TCGA-DH-A669 TCGA-DH-A66G TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6407 
       25.48        30.21        17.19         1.22         7.04        94.52 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 TCGA-E1-A7YI TCGA-E1-A7YQ TCGA-E1-A7YS 
        5.10        23.74        17.98         3.65        51.88        15.32 
TCGA-E1-A7Z4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-A70Y TCGA-HT-7692 
      145.05        25.48        36.82        42.54        28.54         2.96 
TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A614 
       19.23        23.61        11.28        15.72         0.23         2.70 
TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7493 TCGA-HW-8322 TCGA-IK-7675 TCGA-P5-A5EZ 
       16.14        11.05        69.27        24.92        19.00         2.30 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-S9-A6TV TCGA-S9-A6TZ 
        7.59         1.28        19.33        12.23        18.77        36.82 
TCGA-S9-A7IS TCGA-TM-A7CF TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 
        7.92        65.39        25.87        61.41        26.99        45.93 
TCGA-VM-A8CD 
        7.89 

$`DEL PEAK 11(6P25.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       21.40        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       36.36        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        26.76        37.38        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        91.13 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       39.78        37.45        72.95        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
       63.88        46.06        24.59        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       23.21        17.46        13.71        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 
       49.02        75.16        46.06        65.75        87.45        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83       114.08         7.96         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       154.36        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       29.85        31.69        24.43        26.17        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       25.55        21.57        95.11        20.98        22.29        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       26.76        21.30       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
        7.50        44.42        38.89         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YK 
      130.78        14.30        29.13        93.21        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW 
       16.18        21.30        75.02         0.76        32.45        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      146.14        13.08        73.48        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 
        0.20        47.77        52.21        18.77        14.93        41.33 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       28.34        13.68        14.24        16.01        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.76        21.53        15.02        16.44        22.26        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       36.66        48.69         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
       31.69        14.96         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        3.72        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       34.19        28.27        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       27.35         0.10         5.33        16.93         1.81        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O 
       17.52        17.65         2.43        10.52        15.35         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       56.58        45.44        41.49        68.32        35.44        39.75 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       40.01        42.54        31.63        12.76        28.87        20.71 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        9.44         5.88         7.96         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       41.10        40.93        35.38        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       20.68        15.06        18.54        28.37        27.16       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       20.48        54.77        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RU TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       33.93        31.36        43.20        13.51         0.10        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                       145.05                        211.17 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                        19.33                         22.42 
[1] "0.2 - 145.1 (19.3)" "0.0 - 211.2 (22.4)"
[1] "hr=" "2.3"
D31V2, continuous
D31V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED    22  28
  DEL PEAK 11(6P25.3) WILD-TYPE 206 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     22   28
  DEL PEAK 11(6P25.3) WILD-TYPE  206  256
        clus
vv       DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  FEMALE                          22                           206
  MALE                            28                           256
[1] 2 2
[1] FALSE
D31V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED    12  30
  DEL PEAK 11(6P25.3) WILD-TYPE 172 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     12   30
  DEL PEAK 11(6P25.3) WILD-TYPE  172  265
     clus
vv    DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  NO                           12                           172
  YES                          30                           265
[1] 2 2
[1] FALSE
D31V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 11(6P25.3) MUTATED            24               10                16
  DEL PEAK 11(6P25.3) WILD-TYPE         170              119               173
D31V6, multiclass
                   clus
vv                  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  ASTROCYTOMA                                24                           170
  OLIGOASTROCYTOMA                           10                           119
  OLIGODENDROGLIOMA                          16                           173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6P25.3) MUTATED                                  1     0
  DEL PEAK 11(6P25.3) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6P25.3) MUTATED                           2    47
  DEL PEAK 11(6P25.3) WILD-TYPE                        19   425
D31V7, multiclass
                                  clus
vv                                 DEL PEAK 11(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     47
                                  clus
vv                                 DEL PEAK 11(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      425
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED     5  42
  DEL PEAK 11(6P25.3) WILD-TYPE  27 404
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED      5   42
  DEL PEAK 11(6P25.3) WILD-TYPE   27  404
                        clus
vv                       DEL PEAK 11(6P25.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK 11(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                27
  NOT HISPANIC OR LATINO                           404
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 12(6Q22.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(6Q22.31) MUTATED    48  28
  DEL PEAK 12(6Q22.31) WILD-TYPE 335  97
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            76                            432 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            28                             97 
$`DEL PEAK 12(6Q22.31) MUTATED`
TCGA-DH-A66B TCGA-HT-A619 TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 
       42.05        21.40        60.10         6.38        46.95        36.56 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A75M TCGA-DH-A669 TCGA-DU-5847 
       33.57        31.63        25.48        17.88        30.21        18.02 
TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 
        6.81        17.49         1.22        19.89         2.40        11.47 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 
        6.54       117.40        18.94         5.10        23.74        17.98 
TCGA-DU-A7TC TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YK TCGA-E1-A7YQ 
       37.38        41.13        79.99        57.93        12.43        51.88 
TCGA-E1-A7YS TCGA-E1-A7Z2 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A4MT 
       15.32        13.08        25.48        17.88        32.61        38.27 
TCGA-FG-A6J3 TCGA-FN-7833 TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 
       22.26        27.52        17.42        17.29        31.69        14.96 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB 
        2.96        19.23        11.28        15.72         0.23         0.10 
TCGA-HT-A617 TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 
       16.14        12.76         0.23         2.30         7.96         7.59 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A780 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A870 
        1.28        10.42         2.37        19.33        12.23        12.99 
TCGA-RY-A83Z TCGA-S9-A6TZ TCGA-S9-A6U6 TCGA-S9-A7IS TCGA-S9-A7R2 TCGA-S9-A7R3 
        9.90        36.82        35.15         7.92        10.39        99.06 
TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q TCGA-TQ-A7RF TCGA-TQ-A7RW TCGA-TQ-A8XE 
       31.59        65.39        25.38        21.37        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-WY-A85B 
       45.93         7.89        20.02        45.80 

$`DEL PEAK 12(6Q22.31) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 
       23.90        20.09        17.82        20.45        18.64        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.26        21.01        53.62        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        48.30        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        50.86        91.13        44.52 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        24.20        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       13.71        18.61        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        8.45       182.33        18.94        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96        62.96       156.23       154.36        14.99       105.21 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       94.32        44.02        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
        2.76        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 
       20.98        22.29        11.41        26.76        21.30       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       84.33        51.52         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       50.14        67.46       134.27        78.21        95.57       130.78 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL 
       14.30        29.13        93.21         3.65        19.46        16.18 
TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       21.30        75.02         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        52.21        36.82        18.77        14.93        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       41.33        18.44        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 
       28.34        13.68        14.24        16.01        14.96        22.52 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        14.76        21.53 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.03        16.54         3.75         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        5.03        29.85        23.18       122.47         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        3.72        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       34.19        28.27        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       27.35         5.33         2.70        16.93         1.81        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW 
       28.87        20.71        19.00        14.40        14.40         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A72X 
        7.99         2.37         9.44         5.88         0.23        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       12.23        19.20         3.45         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        15.85        14.04        14.83        14.53        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       13.41         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
        1.91        16.50        16.70        11.08        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       32.65        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       35.38        24.39        25.81        29.85        32.61        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        14.07        36.13        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        20.68        15.06        18.54 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
       28.37        27.16       169.84        30.05        98.63        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       20.48        54.77        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       61.41        43.20        13.51         0.10        39.16        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        39.88        43.40        46.88        37.71        20.81 

  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                        117.40                         211.17 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                         18.48                          23.49 
[1] "0.1 - 117.4 (18.5)" "0.0 - 211.2 (23.5)"
[1] "hr=" "2.5"
D32V2, continuous
D32V3, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED    38  39
  DEL PEAK 12(6Q22.31) WILD-TYPE 190 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED     38   39
  DEL PEAK 12(6Q22.31) WILD-TYPE  190  245
        clus
vv       DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  FEMALE                           38                            190
  MALE                             39                            245
[1] 2 2
[1] FALSE
D32V4, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED    16  53
  DEL PEAK 12(6Q22.31) WILD-TYPE 168 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED     16   53
  DEL PEAK 12(6Q22.31) WILD-TYPE  168  242
     clus
vv    DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  NO                            16                            168
  YES                           53                            242
[1] 2 2
[1] FALSE
D32V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 12(6Q22.31) MUTATED            47               11                19
  DEL PEAK 12(6Q22.31) WILD-TYPE         147              118               170
D32V6, multiclass
                   clus
vv                  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  ASTROCYTOMA                                 47                            147
  OLIGOASTROCYTOMA                            11                            118
  OLIGODENDROGLIOMA                           19                            170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q22.31) MUTATED                                  1     1
  DEL PEAK 12(6Q22.31) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q22.31) MUTATED                           5    70
  DEL PEAK 12(6Q22.31) WILD-TYPE                        16   402
D32V7, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      70
                                  clus
vv                                 DEL PEAK 12(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED     4  66
  DEL PEAK 12(6Q22.31) WILD-TYPE  28 380
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED      4   66
  DEL PEAK 12(6Q22.31) WILD-TYPE   28  380
                        clus
vv                       DEL PEAK 12(6Q22.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       DEL PEAK 12(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 28
  NOT HISPANIC OR LATINO                            380
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    52  28
  DEL PEAK 13(6Q26) WILD-TYPE 331  97
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         80                         428 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         28                          97 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-DH-A66B TCGA-HT-A619 TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 
       42.05        21.40        60.10         6.38        46.95        36.56 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A75M TCGA-DH-A669 TCGA-DU-5847 
       33.57        31.63        25.48        17.88        30.21        18.02 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 
        8.45         6.81        17.49         1.22        19.89         2.40 
TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 
       11.47         6.54       117.40        18.94         5.10        23.74 
TCGA-DU-A7T6 TCGA-DU-A7TC TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YJ TCGA-E1-A7YK 
       17.98        37.38        57.93       130.78        19.46        12.43 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-FG-5963 TCGA-FG-7636 
       51.88        15.32        13.08       145.05        25.48        17.88 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7475 
       32.61        38.27        22.26        27.52         0.03        17.42 
TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7884 
       17.29        31.69        14.96         2.96        19.23        11.28 
TCGA-HT-8108 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-A5KK 
        2.50        15.72         0.23         0.10        16.14        12.76 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        0.23         2.30         7.96         7.59         1.28        10.42 
TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A870 TCGA-S9-A6TZ 
        7.56         2.37        19.33        12.23        12.99        36.82 
TCGA-S9-A6U6 TCGA-S9-A7IX TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q 
       35.15        26.93        99.06        31.59        65.39        25.38 
TCGA-TQ-A7RF TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-VM-A8CF 
       21.37        26.99        31.36        45.93         7.89        20.02 
TCGA-VV-A86M TCGA-WY-A85B 
       16.01        45.80 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.88        46.72        31.82        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HW-7490 
       23.90        20.09        17.82        20.45        18.64        45.60 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 
       42.77        59.38       117.50         7.69        43.89        36.36 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.26        21.01        53.62        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        48.30        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        50.86        91.13        44.52 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        24.20        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       13.71        18.61        14.56        17.46         6.74        13.38 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        16.83        94.52       114.08         7.96 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 
       62.96       156.23       154.36        14.99       105.21         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       24.99        33.96        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       22.29        11.41        26.76        21.30       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       51.52         7.50        44.42        38.89         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YL TCGA-E1-A7YM 
       14.30        29.13        93.21         3.65        16.18        21.30 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 
       75.02         0.76        32.45        36.82       146.14        73.48 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        47.77        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW 
       14.24        16.01        14.96        22.52        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7467 
       28.54        10.78        36.66        48.69         5.72         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54        40.11         0.13        16.54         3.75 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.10         0.46         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59        34.19        28.27        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07        27.35         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       24.92        31.63        28.87        20.71        19.00        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         6.71         7.99         2.37         9.44         5.88 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        9.60        12.23        19.20         3.45         4.41        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       16.73         1.91        16.50        16.70        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       94.03        32.65        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       41.10        40.93        35.38        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      135.22        85.55        38.56        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       169.84        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        18.71        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        23.80        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8C9 TCGA-VM-A8CA 
       26.14        25.87        33.93        61.41        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI 
        0.10        39.16        23.47        37.05        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C 
       51.06        13.32        43.96        39.88        43.40        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     145.05                      211.17 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      18.48                       23.56 
[1] "0.0 - 145.1 (18.5)" "0.1 - 211.2 (23.6)"
[1] "hr=" "2.1"
D33V2, continuous
D33V3, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    41  40
  DEL PEAK 13(6Q26) WILD-TYPE 187 244
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     41   40
  DEL PEAK 13(6Q26) WILD-TYPE  187  244
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  FEMALE                        41                         187
  MALE                          40                         244
[1] 2 2
[1] FALSE
D33V4, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    18  54
  DEL PEAK 13(6Q26) WILD-TYPE 166 241
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     18   54
  DEL PEAK 13(6Q26) WILD-TYPE  166  241
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         18                         166
  YES                        54                         241
[1] 2 2
[1] FALSE
D33V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 13(6Q26) MUTATED            48               12                21
  DEL PEAK 13(6Q26) WILD-TYPE         146              117               168
D33V6, multiclass
                   clus
vv                  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  ASTROCYTOMA                              48                         146
  OLIGOASTROCYTOMA                         12                         117
  OLIGODENDROGLIOMA                        21                         168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  1     1
  DEL PEAK 13(6Q26) WILD-TYPE                                0     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q26) MUTATED                           5    73
  DEL PEAK 13(6Q26) WILD-TYPE                        16   399
D33V7, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   73
                                  clus
vv                                 DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    399
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED     5  69
  DEL PEAK 13(6Q26) WILD-TYPE  27 377
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      5   69
  DEL PEAK 13(6Q26) WILD-TYPE   27  377
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             5                          27
  NOT HISPANIC OR LATINO                        69                         377
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 14(7P22.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7P22.3) MUTATED    14   9
  DEL PEAK 14(7P22.3) WILD-TYPE 369 116
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           23                           485 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                            9                           116 
$`DEL PEAK 14(7P22.3) MUTATED`
TCGA-E1-A7YN TCGA-CS-5393 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-7304 TCGA-DU-A6S7 
       23.90        40.18        46.06        65.75        23.31        20.98 
TCGA-DU-A76R TCGA-FG-8188 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7477 TCGA-HW-A5KL 
       21.30        14.96        27.52        40.11        24.26        28.87 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A780 TCGA-QH-A6CX TCGA-S9-A6TS TCGA-S9-A7R3 
        7.96         1.28         2.37        12.23        62.17        99.06 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TQ-A7RM TCGA-TQ-A8XE TCGA-VW-A7QS 
       40.64        30.44        36.69        31.36        23.21 

$`DEL PEAK 14(7P22.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       17.16        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       36.36        60.10         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       46.06        24.59        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        23.21        17.46        13.71        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         2.40        11.47        62.96       156.23       154.36 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       44.02        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       26.17        24.99        33.96        25.55        21.57        95.11 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       22.29        11.41        26.76        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ 
       51.52        37.38         7.50        44.42        38.89         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO 
        3.65        19.46        12.43        16.18        21.30        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY 
       51.88        15.32         0.76        32.45        36.82       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        52.21        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        42.54        41.33        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       22.26        28.54        10.78        36.66        48.69         5.72 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       68.32        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       24.92        31.63        12.76        20.71        19.00        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         7.99         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        9.44         5.88         7.59         0.23        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       11.64        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
       12.23        19.20         3.45         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
       28.08         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        40.93        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        26.93        23.51        19.99        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       27.16       169.84        10.39        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        20.48        54.77        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J 
       65.39        24.92        16.18        59.05        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR 
       44.09        33.73        31.20        30.05        26.14        25.87 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       33.93        61.41        26.99        45.93        43.20        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                         1.28                          0.03 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        99.06                        211.17 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        27.52                         21.53 
[1] "1.3 - 99.1 (27.5)"  "0.0 - 211.2 (21.5)"
[1] "hr=" "1.7"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED    12  11
  DEL PEAK 14(7P22.3) WILD-TYPE 216 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED     12   11
  DEL PEAK 14(7P22.3) WILD-TYPE  216  273
        clus
vv       DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  FEMALE                          12                           216
  MALE                            11                           273
[1] 2 2
[1] FALSE
D34V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     5  17
  DEL PEAK 14(7P22.3) WILD-TYPE 179 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      5   17
  DEL PEAK 14(7P22.3) WILD-TYPE  179  278
     clus
vv    DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  NO                            5                           179
  YES                          17                           278
[1] 2 2
[1] FALSE
D34V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 14(7P22.3) MUTATED            10                5                 8
  DEL PEAK 14(7P22.3) WILD-TYPE         184              124               181
D34V6, multiclass
                   clus
vv                  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  ASTROCYTOMA                                10                           184
  OLIGOASTROCYTOMA                            5                           124
  OLIGODENDROGLIOMA                           8                           181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(7P22.3) MUTATED                                  0     1
  DEL PEAK 14(7P22.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(7P22.3) MUTATED                           0    22
  DEL PEAK 14(7P22.3) WILD-TYPE                        21   450
D34V7, multiclass
                                  clus
vv                                 DEL PEAK 14(7P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     22
                                  clus
vv                                 DEL PEAK 14(7P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      450
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     2  19
  DEL PEAK 14(7P22.3) WILD-TYPE  30 427
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      2   19
  DEL PEAK 14(7P22.3) WILD-TYPE   30  427
                        clus
vv                       DEL PEAK 14(7P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK 14(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                30
  NOT HISPANIC OR LATINO                           427
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 15(8Q24.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8Q24.3) MUTATED    22   7
  DEL PEAK 15(8Q24.3) WILD-TYPE 361 118
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           29                           479 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                            7                           118 
$`DEL PEAK 15(8Q24.3) MUTATED`
TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A7UU TCGA-DU-7006 TCGA-DU-7301 
       78.28        18.51        19.96        13.71        11.47        25.91 
TCGA-DU-8165 TCGA-DU-A7TJ TCGA-E1-A7YD TCGA-E1-A7YI TCGA-E1-A7YQ TCGA-FG-5965 
       19.13         0.56        14.30         3.65        51.88        36.82 
TCGA-FG-8185 TCGA-FG-A4MY TCGA-FG-A70Y TCGA-HT-7473 TCGA-HT-7610 TCGA-HT-7688 
       14.24        23.70        28.54        16.54        56.09        31.69 
TCGA-HT-7879 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HW-8321 TCGA-P5-A5F6 
        3.68         0.23        15.72         0.23        42.54         1.28 
TCGA-QH-A6CV TCGA-S9-A6WM TCGA-VM-A8C8 TCGA-WY-A859 TCGA-WY-A85E 
       14.53        19.86        45.93        39.88        20.81 

$`DEL PEAK 15(8Q24.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       43.89        36.36        60.10        40.18         0.26        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 
       53.62         6.38        17.69        26.76        37.38        46.95 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
       48.30        49.94        49.12       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       47.93        72.92        50.86        91.13        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        63.88        46.06 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       24.59        30.21        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       23.21        17.46        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         2.40        62.96       156.23       154.36        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       33.96        25.55        21.57        95.11        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        21.30        17.98       139.04        84.33 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
       51.52        37.38         7.50        44.42        38.89        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YK 
       95.57       130.78        29.13        93.21        19.46        12.43 
TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YV 
       16.18        21.30        75.02        15.32         0.76        32.45 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       36.82       146.14        13.08        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.38        18.71        14.76        21.53        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 
       22.26        10.78        36.66        48.69         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
        0.49        23.61        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        34.19        28.27        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
        1.81        16.14        16.83        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        56.58        45.44 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       41.49        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       24.92        31.63        12.76        28.87        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         7.99         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.30         9.44         5.88         7.96         7.59         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23        13.41         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.70        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
      135.22        85.55        38.56        84.99        31.10        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        18.64        14.07        36.13         7.92        26.93 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51        19.99        20.02         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       23.80        21.37        19.69        15.98         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C9 
       25.87        33.93        61.41        26.99        31.36        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       13.51         0.10         7.89        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        43.40        45.80        46.88        37.71 

  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                        78.28                        211.17 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                        19.13                         23.18 
[1] "0.2 - 78.3 (19.1)"  "0.0 - 211.2 (23.2)"
[1] "hr=" "1.5"
D35V2, continuous
D35V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED    15  14
  DEL PEAK 15(8Q24.3) WILD-TYPE 213 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED     15   14
  DEL PEAK 15(8Q24.3) WILD-TYPE  213  270
        clus
vv       DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  FEMALE                          15                           213
  MALE                            14                           270
[1] 2 2
[1] FALSE
D35V4, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED     7  19
  DEL PEAK 15(8Q24.3) WILD-TYPE 177 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED      7   19
  DEL PEAK 15(8Q24.3) WILD-TYPE  177  276
     clus
vv    DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  NO                            7                           177
  YES                          19                           276
[1] 2 2
[1] FALSE
D35V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 15(8Q24.3) MUTATED            12               10                 7
  DEL PEAK 15(8Q24.3) WILD-TYPE         182              119               182
D35V6, multiclass
                   clus
vv                  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  ASTROCYTOMA                                12                           182
  OLIGOASTROCYTOMA                           10                           119
  OLIGODENDROGLIOMA                           7                           182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8Q24.3) MUTATED                                  0     1
  DEL PEAK 15(8Q24.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8Q24.3) MUTATED                           2    26
  DEL PEAK 15(8Q24.3) WILD-TYPE                        19   446
D35V7, multiclass
                                  clus
vv                                 DEL PEAK 15(8Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     26
                                  clus
vv                                 DEL PEAK 15(8Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      446
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED     3  23
  DEL PEAK 15(8Q24.3) WILD-TYPE  29 423
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED      3   23
  DEL PEAK 15(8Q24.3) WILD-TYPE   29  423
                        clus
vv                       DEL PEAK 15(8Q24.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       DEL PEAK 15(8Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                29
  NOT HISPANIC OR LATINO                           423
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 16(9P23) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(9P23) MUTATED    94  54
  DEL PEAK 16(9P23) WILD-TYPE 289  71
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        148                         360 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                         54                          71 
$`DEL PEAK 16(9P23) MUTATED`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-E1-A7YN TCGA-HW-7490 TCGA-CS-4943 TCGA-CS-5393 
       46.88        46.72        23.90        45.60        36.36        40.18 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6666 TCGA-DB-5277 
       21.01        53.62         6.38        26.76        46.95        50.86 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L 
       44.52        78.28        30.21        33.57        31.63        24.20 
TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-A7UR TCGA-DU-5847 
        5.98        29.23        11.24        16.18        54.25        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 
       17.46         6.74         8.45         6.81        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 
       65.75         7.04        11.64        19.89         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 
       62.96       117.40        90.77        26.30         7.96        18.94 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8168 
       25.91        23.31        41.98        23.74        14.60        14.17 
TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD 
       33.96        20.98        22.29        17.98        84.33         7.50 
TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YE 
        0.56        41.13        79.99        57.93        14.30        29.13 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YV 
        3.65        19.46        21.30        51.88        15.32        32.45 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       13.08        73.48        39.48         0.20        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MW 
       36.82        42.54        18.44        17.88        14.24        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7470 
       18.71        23.70        22.26        48.69         5.72        40.11 
TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7606 TCGA-HT-7687 
        0.13        17.42         6.54        24.26        17.29         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7902 TCGA-HT-8104 
       31.69        14.96         2.96        19.23        31.43        12.23 
TCGA-HT-8108 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A618 TCGA-HT-A74J 
        2.50        27.35         0.10         2.70        16.83        10.52 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EV 
       39.75        40.01        24.92        20.71        14.40         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-P5-A780 
        2.30         7.96         7.59         1.28        11.64         2.37 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-RY-A83Z TCGA-S9-A6TS 
       14.53        12.23         9.17         1.91         9.90        62.17 
TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ 
       41.10        38.56        18.64         7.92        26.93        19.99 
TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84H 
       20.02       169.84        99.06        31.59        65.39        30.44 
TCGA-TM-A84J TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-TQ-A7RP TCGA-TQ-A7RV TCGA-TQ-A7RW 
       24.16        25.38        15.98        30.05        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VV-A829 
       31.36        45.93         0.10         7.89        20.02        37.05 
TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 
       16.01        51.06        13.32        39.88 

$`DEL PEAK 16(9P23) WILD-TYPE`
TCGA-CS-6665 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 
       51.55        31.82        42.05        62.01        17.16        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M 
       17.82        20.45        18.64        21.40        42.77        59.38 
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6186 
      117.50         7.69        43.89        60.10         0.26        17.69 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        48.30        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 
       75.25        47.93        72.92        91.13        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P 
       18.84        39.78        37.45        72.95        25.48        30.12 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        14.40        18.51        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        19.96        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       30.21        27.81        17.19        17.19        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 
       13.71        18.61        14.56        13.38       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 
       17.49        15.16       211.17        52.11        22.42        75.16 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        1.22        87.45       133.74        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
        7.96       156.23       154.36        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 
        8.84        30.67        10.36        94.32        44.02        60.30 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
        2.76         5.10        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
       24.99        25.55        21.57        95.11        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI 
       21.30       139.04        51.52        37.38        44.42        38.89 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       50.14        67.46       134.27        78.21        95.57       130.78 
TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YW 
       93.21        12.43        16.18        75.02         0.76        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-6688 
      146.14       145.05        32.35         0.23        47.77        18.77 
TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       14.93        41.33        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       28.34        13.68        16.01        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       38.27        10.72        14.76        21.53        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       28.54        10.78        36.66        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 
       11.54         0.03        16.54         3.75         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18       122.47         4.57         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 
       33.01         6.25         0.10         0.46         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A615 
       26.04         0.13        20.22         0.07         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K 
        1.81        16.14        17.52        17.65         2.43        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       69.27        35.44        42.54        31.63        12.76        28.87 
TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       19.00        14.40         6.71         7.99         2.37         9.44 
TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 
        5.88         0.23        10.42        13.25        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       13.61         9.60         7.56        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        14.83        13.61        13.41        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        19.59        30.67        87.12        18.77        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       35.15        98.24        95.93         5.85       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
      135.22        85.55        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.61        14.07        36.13        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
       20.68        15.06        18.54        28.37        27.16        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        18.71        20.48        54.77        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       28.08        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       23.80        21.37        19.69         2.04        40.41        44.09 
TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       36.69        33.73        31.20        26.14        25.87        33.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VW-A7QS TCGA-VW-A8FI 
       43.20        13.51        39.16        23.47        23.21         8.05 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     169.84                      211.17 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     21.780                      22.535 
[1] "0.1 - 169.8 (21.8)" "0.0 - 211.2 (22.5)"
[1] "hr=" "2.4"
D36V2, continuous
D36V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    70  79
  DEL PEAK 16(9P23) WILD-TYPE 158 205
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     70   79
  DEL PEAK 16(9P23) WILD-TYPE  158  205
        clus
vv       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  FEMALE                        70                         158
  MALE                          79                         205
[1] 2 2
[1] FALSE
D36V4, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    33 102
  DEL PEAK 16(9P23) WILD-TYPE 151 193
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     33  102
  DEL PEAK 16(9P23) WILD-TYPE  151  193
     clus
vv    DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  NO                         33                         151
  YES                       102                         193
[1] 2 2
[1] FALSE
D36V5, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 16(9P23) MUTATED            72               33                44
  DEL PEAK 16(9P23) WILD-TYPE         122               96               145
D36V6, multiclass
                   clus
vv                  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  ASTROCYTOMA                              72                         122
  OLIGOASTROCYTOMA                         33                          96
  OLIGODENDROGLIOMA                        44                         145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P23) MUTATED                                  0     2
  DEL PEAK 16(9P23) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P23) MUTATED                           8   134
  DEL PEAK 16(9P23) WILD-TYPE                        13   338
D36V7, multiclass
                                  clus
vv                                 DEL PEAK 16(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                8
  WHITE                                                  134
                                  clus
vv                                 DEL PEAK 16(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED     9 128
  DEL PEAK 16(9P23) WILD-TYPE  23 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED      9  128
  DEL PEAK 16(9P23) WILD-TYPE   23  318
                        clus
vv                       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  HISPANIC OR LATINO                             9                          23
  NOT HISPANIC OR LATINO                       128                         318
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 17(9P21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9P21.3) MUTATED   105  69
  DEL PEAK 17(9P21.3) WILD-TYPE 278  56
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          174                           334 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                           69                            56 
$`DEL PEAK 17(9P21.3) MUTATED`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-E1-A7YN TCGA-FG-A87N TCGA-HW-7490 TCGA-CS-4943 
       46.88        46.72        23.90        18.64        45.60        36.36 
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18        21.01        53.62         6.38        17.69        26.76 
TCGA-CS-6666 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB 
       46.95        47.93        50.86        44.52        78.28        30.21 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64V TCGA-DB-A75L TCGA-DB-A75P 
       33.57        31.63        24.20        29.23        11.24        16.18 
TCGA-DH-5140 TCGA-DH-A7UR TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 
       19.96        54.25        18.02        17.46         6.74         8.45 
TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 
        6.81        49.02        46.06        65.75         7.04        11.64 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       19.89        16.83        94.52         2.40        11.47        62.96 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        6.54       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 
       18.94        25.91        60.30        23.31        41.98         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 
       23.74        14.60        14.17        33.96        20.98        22.29 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ 
       11.41        26.76        17.98        84.33         7.50         0.56 
TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ 
       41.13        57.93        14.30        29.13         3.65        19.46 
TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       21.30        51.88        15.32        32.45        13.08        73.48 
TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 
       39.48         0.20        25.48        52.21        36.82        42.54 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       18.44        17.88        14.24        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q 
       23.70        22.26        28.54        10.78        48.69         5.72 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
       11.54        40.11         0.13        17.42         6.54        24.26 
TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.29         0.10        31.69        14.96         2.96        19.23 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8108 
        0.23         0.49        31.43        16.24        12.23         2.50 
TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       13.78         0.23        27.35         0.10         5.33         2.70 
TCGA-HT-A61C TCGA-HT-A74J TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KK 
       17.65        10.52        39.75        40.01        24.92        12.76 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 
       20.71        19.00        14.40         0.23         2.30         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z TCGA-P5-A780 TCGA-QH-A6CV 
        7.59         1.28         0.23        11.64         2.37        14.53 
TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-RY-A83Z TCGA-S9-A6TS 
       12.23         9.17         1.91        16.70         9.90        62.17 
TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7IS 
       41.10        24.39         5.85        38.56        19.86         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 
       26.93        19.99        20.02       169.84        99.06        31.59 
TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RP 
       20.48        65.39        30.44        24.16        15.98        30.05 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CF 
       26.99        31.36        45.93         0.10         7.89        20.02 
TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85B 
       16.01        51.06        13.32        43.96        39.88        45.80 

$`DEL PEAK 17(9P21.3) WILD-TYPE`
TCGA-CS-6665 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 
       51.55        31.82        42.05        62.01        17.16        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 
       17.82        20.45        21.40        42.77        59.38       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6290 TCGA-CS-6667 
        7.69        43.89        60.10         0.26        37.38        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 
       49.94        49.12       122.73        81.96        75.25        72.92 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE 
       91.13        36.56        46.42        18.84        39.78        37.45 
TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O 
       27.81        14.40        18.51        12.10        17.88        30.74 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       63.88        46.06        24.59        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 
       17.19        23.21        17.46        13.71        18.61        14.56 
TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
       13.38       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 
       52.11        22.42        75.16         1.22        87.45       133.74 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
      114.08         7.96       156.23       154.36        14.99       105.21 
TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7309 TCGA-DU-8163 
        8.84        10.36        94.32        44.02         2.76        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       31.69        24.43        26.17        24.99        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       95.11        21.30       139.04        51.52        37.38        44.42 
TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       38.89        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO 
       95.57       130.78        93.21        12.43        16.18        75.02 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O3 
        0.76        36.82       146.14       145.05        32.35         0.23 
TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 
       47.77        18.77        14.93        41.33        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8188 
       20.61        20.09        28.34        13.68        16.01        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       22.52        32.61        38.27        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 
       16.44        36.66        27.52         0.10         6.67         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       16.54         3.75         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       44.68         6.05        42.74         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 
        6.90        14.53        39.48        39.09        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
        3.72        11.28         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01         6.25         0.10         0.46         5.56 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59        34.19        28.27        15.72        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.13        20.22         0.07        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       16.83        17.52         2.43        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       56.58        45.44        41.49        68.32        69.27        35.44 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX 
       42.54        31.63        28.87        14.40         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 
        2.37         9.44         5.88        10.42        13.25        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X3 
       14.04        19.33        14.83        13.61        13.41        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
       14.53        16.34        16.73        16.50        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        19.59        30.67        87.12        18.77        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       35.38        36.82        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       36.13        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.54        28.37        27.16        10.39        30.05        98.63 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       18.71        54.77        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M 
       16.18        59.05        40.64        28.08        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       19.69         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8C9 
       31.20        26.14        25.87        33.93        61.41        43.20 
TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI 
       13.51        39.16        23.47        37.05        23.21         8.05 
TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        46.88        37.71        20.81 

  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       169.84                        211.17 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       19.975                        24.115 
[1] "0.1 - 169.8 (20.0)" "0.0 - 211.2 (24.1)"
[1] "hr=" "3.5"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    85  90
  DEL PEAK 17(9P21.3) WILD-TYPE 143 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     85   90
  DEL PEAK 17(9P21.3) WILD-TYPE  143  194
        clus
vv       DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  FEMALE                          85                           143
  MALE                            90                           194
[1] 2 2
[1] FALSE
D37V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    36 121
  DEL PEAK 17(9P21.3) WILD-TYPE 148 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     36  121
  DEL PEAK 17(9P21.3) WILD-TYPE  148  174
     clus
vv    DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  NO                           36                           148
  YES                         121                           174
[1] 2 2
[1] FALSE
D37V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 17(9P21.3) MUTATED            85               36                54
  DEL PEAK 17(9P21.3) WILD-TYPE         109               93               135
D37V6, multiclass
                   clus
vv                  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  ASTROCYTOMA                                85                           109
  OLIGOASTROCYTOMA                           36                            93
  OLIGODENDROGLIOMA                          54                           135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(9P21.3) MUTATED                                  0     3
  DEL PEAK 17(9P21.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P21.3) MUTATED                          10   158
  DEL PEAK 17(9P21.3) WILD-TYPE                        11   314
D37V7, multiclass
                                  clus
vv                                 DEL PEAK 17(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    158
                                  clus
vv                                 DEL PEAK 17(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED     9 152
  DEL PEAK 17(9P21.3) WILD-TYPE  23 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED      9  152
  DEL PEAK 17(9P21.3) WILD-TYPE   23  294
                        clus
vv                       DEL PEAK 17(9P21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         152
                        clus
vv                       DEL PEAK 17(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                23
  NOT HISPANIC OR LATINO                           294
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 18(10Q26.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(10Q26.3) MUTATED    82  68
  DEL PEAK 18(10Q26.3) WILD-TYPE 301  57
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           150                            358 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                            68                             57 
$`DEL PEAK 18(10Q26.3) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-CS-4941 TCGA-CS-5395 
       51.55        42.05        23.90        18.64         7.69        21.01 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF 
        6.38        17.69        26.76        50.86        44.52        33.57 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-A669 TCGA-DH-A66D 
       24.20        25.48        11.24        19.96        30.21        27.81 
TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5872 
       13.71        18.02         6.74        13.38         8.45        17.49 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 
       75.16        65.75        87.45         7.04        11.64        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       16.83        94.52       114.08        11.47        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7290 
       14.99         6.54         8.84       117.40        90.77        10.36 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
        7.96        18.94        25.91         5.10        23.74        14.60 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       19.13        15.48        33.96        11.41        26.76        21.30 
TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5311 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI 
        7.50         0.56       134.27        14.30        29.13         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7Z2 
       19.46        16.18        21.30        51.88        32.45        13.08 
TCGA-E1-A7Z4 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8188 TCGA-FG-A4MU 
      145.05        18.77        18.44        20.09        14.96        10.72 
TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7469 
       18.38        22.26        10.78        48.69         5.72        11.54 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7606 
        0.13        16.54         6.54       172.77         4.01        17.29 
TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7873 
       31.69         0.10        17.52         0.23         0.49        23.61 
TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8108 
        3.68         3.72        31.43        16.24        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-HT-A5RA 
       13.78        28.27        15.72         0.23        20.22        27.35 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-8321 TCGA-HW-A5KK 
        5.33        16.14        17.65         2.43        42.54        12.76 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72W 
       19.00        14.40         2.30         7.96         0.23        10.42 
TCGA-P5-A780 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 
        2.37        19.33        14.53        12.23        10.29         1.91 
TCGA-QH-A6XC TCGA-RY-A83X TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UB 
       16.70        30.87         9.90        62.17        24.39       123.65 
TCGA-S9-A6WM TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7QW 
       19.86        14.07         7.92        26.93        20.02        15.06 
TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7CF 
       18.54        10.39        99.06        20.48        54.77        65.39 
TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RF TCGA-TQ-A7RJ TCGA-TQ-A7RM 
       24.92        28.08        24.16        21.37        40.41        36.69 
TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-VM-A8CD TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A85D 
       30.05        25.87         7.89         8.05        13.32        37.71 

$`DEL PEAK 18(10Q26.3) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 
       46.88        46.72        31.82        62.01        17.16        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M 
       17.82        20.45        21.40        45.60        42.77        59.38 
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 
      117.50        43.89        36.36        60.10        40.18         0.26 
TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       53.62        37.38        46.95        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        91.13 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       36.56        78.28        46.42        18.84        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       37.45        72.95        31.63        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       17.88        30.74        16.18        63.88        46.06        24.59 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       17.19        17.19        54.25        23.21        17.46        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 
       14.56        17.46         6.81       182.33        18.94        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 
      211.17        52.11        22.42        49.02        46.06         1.22 
TCGA-DU-6404 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7018 
      133.74         7.96         2.40       154.36       105.21        30.67 
TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       26.30        94.32        44.02        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP 
        2.76        20.68        21.40        16.96        14.17        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       29.85        31.69        24.43        26.17        24.99        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7T8 
       21.57        95.11        20.98        22.29        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
       84.33        51.52        37.38        44.42        38.89        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99        57.93        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
      130.78        93.21        12.43        75.02        15.32         0.76 
TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       36.82       146.14        73.48        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
        0.20        47.77        25.48        52.21        36.82        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       42.54        41.33        15.35        17.88        22.55        20.61 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-8191 
       28.34        13.68        14.24        16.01        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       38.27        18.71        23.70        14.76        21.53        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       16.44        28.54        36.66        27.52         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 
       40.11         0.03         3.75        17.42        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7601 TCGA-HT-7602 
       40.34        75.19        95.93       106.95         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
       39.09        50.63        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       35.47        11.28         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01         6.25         0.10         0.46         5.56 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
        0.23        29.59        34.19        26.04         0.13         0.07 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         2.70        16.93         1.81        16.83        17.52 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        56.58        45.44 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       41.49        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-P5-A5EV 
       24.92        31.63        28.87        20.71        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 
        6.71         7.99         2.37         9.44         5.88         7.59 
TCGA-P5-A5F6 TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        1.28        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 
        9.60         7.56        12.23        19.20         3.45         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        14.04        14.83 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       13.61        13.41         9.17        14.53        16.34        16.73 
TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.50        11.08        12.99        88.83        94.03        32.65 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        5.46        28.08         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 
       18.77        41.10        40.93        35.38        36.82        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7IZ 
       26.47        18.61        18.64        36.13        23.51        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        20.68        28.37        27.16       169.84 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7C5 
       30.05        98.63        31.59        18.71        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       34.78        16.18        59.05        40.64        30.44        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO 
       19.69        15.98         2.04        44.09        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       26.14        33.93        61.41        26.99        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH 
       43.20        13.51         0.10        39.16        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       37.05        16.01        23.21        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       43.40        45.80        46.88        20.81 

  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                        172.77                         211.17 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                         18.20                          26.09 
[1] "0.1 - 172.8 (18.2)" "0.0 - 211.2 (26.1)"
[1] "hr=" "3.7"
D38V2, continuous
D38V3, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED    77  74
  DEL PEAK 18(10Q26.3) WILD-TYPE 151 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED     77   74
  DEL PEAK 18(10Q26.3) WILD-TYPE  151  210
        clus
vv       DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  FEMALE                           77                            151
  MALE                             74                            210
[1] 2 2
[1] FALSE
D38V4, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED    32 109
  DEL PEAK 18(10Q26.3) WILD-TYPE 152 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED     32  109
  DEL PEAK 18(10Q26.3) WILD-TYPE  152  186
     clus
vv    DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  NO                            32                            152
  YES                          109                            186
[1] 2 2
[1] FALSE
D38V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 18(10Q26.3) MUTATED            81               33                37
  DEL PEAK 18(10Q26.3) WILD-TYPE         113               96               152
D38V6, multiclass
                   clus
vv                  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  ASTROCYTOMA                                 81                            113
  OLIGOASTROCYTOMA                            33                             96
  OLIGODENDROGLIOMA                           37                            152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(10Q26.3) MUTATED                                  1     2
  DEL PEAK 18(10Q26.3) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q26.3) MUTATED                           9   138
  DEL PEAK 18(10Q26.3) WILD-TYPE                        12   334
D38V7, multiclass
                                  clus
vv                                 DEL PEAK 18(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                     138
                                  clus
vv                                 DEL PEAK 18(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED     9 136
  DEL PEAK 18(10Q26.3) WILD-TYPE  23 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED      9  136
  DEL PEAK 18(10Q26.3) WILD-TYPE   23  310
                        clus
vv                       DEL PEAK 18(10Q26.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 18(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 23
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 19(11P15.5) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11P15.5) MUTATED    72  31
  DEL PEAK 19(11P15.5) WILD-TYPE 311  94
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                           103                            405 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                            31                             94 
$`DEL PEAK 19(11P15.5) MUTATED`
TCGA-CS-6665 TCGA-CS-4943 TCGA-CS-6290 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-A64X 
       51.55        36.36        37.38        47.93        50.86        18.51 
TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       11.24        19.96        63.88        27.81        17.19        17.46 
TCGA-DH-A7UU TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 
       13.71        17.46        13.38        75.16       114.08        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7298 
       62.96       156.23        14.99       117.40        90.77        18.94 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TR 
        2.76         5.10        19.13        16.96        15.48        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S7 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5304 
       31.69        26.17        20.98        84.33        50.14        41.13 
TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YU TCGA-E1-A7YV 
       29.13         3.65        12.43        16.18         0.76        32.45 
TCGA-E1-A7YW TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-8188 TCGA-FG-A4MW TCGA-FG-A4MY 
       36.82        36.82        14.93        14.96        18.38        23.70 
TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7603 
       21.53        40.11        24.26         6.38         5.03        23.18 
TCGA-HT-7607 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7873 
        3.16         0.16        42.74         0.10        17.52        23.61 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
       31.43        63.55        37.87         0.23        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
       15.72        20.22         2.70         1.81        16.83        17.52 
TCGA-HT-A74O TCGA-HW-7493 TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A735 
        0.10        69.27        39.75        19.00         1.28         9.60 
TCGA-QH-A65S TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7IZ 
        2.53        16.50         9.90        18.77        19.86        19.99 
TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
       20.02        18.54        30.05        98.63        18.71        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RJ 
       54.77        48.33        28.08        24.16        15.98        40.41 
TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-VM-A8CF TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85C 
       25.87        61.41        20.02        13.32        39.88        46.88 
TCGA-WY-A85E 
       20.81 

$`DEL PEAK 19(11P15.5) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        26.76        46.95        48.30        49.94        49.12 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
      122.73        81.96        75.25        72.92        91.13        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       36.56        78.28        46.42        18.84        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       37.45        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5143 
       14.40        12.10        17.88        30.74        16.18        46.06 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UV 
       24.59        30.21        17.19        54.25        23.21        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       18.02        14.56         6.74         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 
        2.40       154.36       105.21         6.54         8.84        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 
       26.30        10.36         7.96        94.32        44.02        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       21.40        14.17        33.27        24.43        24.99        33.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        95.11        22.29        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30        17.98       139.04        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       44.42        38.89         0.56        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YH 
      134.27        78.21        95.57       130.78        14.30        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YY 
       19.46        21.30        75.02        51.88        15.32       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       13.08        73.48       145.05        32.35        39.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 
        0.20        47.77        25.48        52.21        18.77        42.54 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       41.33        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8189 
       20.09        28.34        13.68        14.24        16.01        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6IZ 
       32.61        38.27        10.72        18.71        14.76        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
        5.72        27.52         0.10         6.67        11.54         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.54        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 
       75.19        95.93       106.95       172.77         4.01        29.85 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57        17.29        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 
        6.05         0.10        31.69        14.96         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        9.40         0.10        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-A4DS 
        0.46         2.50         5.56        13.78        29.59         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.93        16.14        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 
       11.05        56.58        45.44        41.49        68.32        35.44 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       40.01        42.54        24.92        31.63        12.76        28.87 
TCGA-HW-A5KM TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        14.40        14.40         0.23         6.71         7.99 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         9.44         5.88         7.96         7.59 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.23        10.42        13.25        11.64        10.95         9.01 
TCGA-P5-A733 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
       13.61         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        4.41        15.16        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23        13.41         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC 
       10.29        14.53        16.34        16.73         1.91        16.70 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        5.46        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       87.12        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       36.13         7.92        26.93        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       20.68        15.06        28.37        27.16       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       99.06        31.59        49.32        34.78        65.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M 
       16.18        59.05        40.64        30.44        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       33.24        25.38        18.61        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
       19.69         2.04        44.09        36.69        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       30.05        26.14        33.93        26.99        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       43.20        13.51         0.10         7.89        39.16        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D 
       43.40        45.80        37.71 

  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                         20.22                          23.21 
[1] "0.1 - 156.2 (20.2)" "0.0 - 211.2 (23.2)"
[1] "hr=" "1.5"
D39V2, continuous
D39V3, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED    54  50
  DEL PEAK 19(11P15.5) WILD-TYPE 174 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED     54   50
  DEL PEAK 19(11P15.5) WILD-TYPE  174  234
        clus
vv       DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  FEMALE                           54                            174
  MALE                             50                            234
[1] 2 2
[1] FALSE
D39V4, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED    25  73
  DEL PEAK 19(11P15.5) WILD-TYPE 159 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED     25   73
  DEL PEAK 19(11P15.5) WILD-TYPE  159  222
     clus
vv    DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  NO                            25                            159
  YES                           73                            222
[1] 2 2
[1] FALSE
D39V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 19(11P15.5) MUTATED            57               30                17
  DEL PEAK 19(11P15.5) WILD-TYPE         137               99               172
D39V6, multiclass
                   clus
vv                  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  ASTROCYTOMA                                 57                            137
  OLIGOASTROCYTOMA                            30                             99
  OLIGODENDROGLIOMA                           17                            172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(11P15.5) MUTATED                                  0     0
  DEL PEAK 19(11P15.5) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11P15.5) MUTATED                           3   100
  DEL PEAK 19(11P15.5) WILD-TYPE                        18   372
D39V7, multiclass
                                  clus
vv                                 DEL PEAK 19(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                     100
                                  clus
vv                                 DEL PEAK 19(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED     7  91
  DEL PEAK 19(11P15.5) WILD-TYPE  25 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED      7   91
  DEL PEAK 19(11P15.5) WILD-TYPE   25  355
                        clus
vv                       DEL PEAK 19(11P15.5) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       DEL PEAK 19(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            355
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 20(11P15.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.1) MUTATED    44  27
  DEL PEAK 20(11P15.1) WILD-TYPE 339  98
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            71                            437 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            27                             98 
$`DEL PEAK 20(11P15.1) MUTATED`
TCGA-CS-6665 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A66G 
       51.55        50.86        19.96        63.88        27.81        17.19 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 
       17.46        13.71        75.16       114.08        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8165 
      156.23        14.99       117.40        90.77         5.10        19.13 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-A7YE 
       29.85        31.69        26.17        50.14        41.13        29.13 
TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-5965 
        3.65        12.43        16.18        32.45        25.48        36.82 
TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 
       14.93        18.38        21.53        40.11        24.26         6.38 
TCGA-HT-7601 TCGA-HT-7607 TCGA-HT-7686 TCGA-HT-7693 TCGA-HT-7873 TCGA-HT-7902 
        5.03         3.16        42.74        17.52        23.61        31.43 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R7 
       63.55        37.87         0.23        28.27        15.72        20.22 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-8319 TCGA-IK-7675 
        2.70         1.81        16.83        17.52        39.75        19.00 
TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-QH-A65S TCGA-RY-A83Z TCGA-S9-A6WM TCGA-S9-A7J0 
        1.28        11.64         2.53         9.90        19.86        20.02 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I 
       98.63        18.71        20.48        54.77        48.33        28.08 
TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RR TCGA-VM-A8CF TCGA-WY-A859 
       24.16        15.98        25.87        20.02        39.88 

$`DEL PEAK 20(11P15.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       36.36        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        6.38        17.69        26.76        37.38        46.95        48.30 
TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       49.94        49.12       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-5144 
       11.24        17.88        30.74        16.18        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UV TCGA-DU-5847 
       30.21        17.19        54.25        23.21        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        7.96         2.40       154.36       105.21         6.54         8.84 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       14.17        33.27        24.43        24.99        33.96        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       21.57        95.11        20.98        22.29        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       139.04        84.33        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42        38.89         0.56        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD 
       57.93       134.27        78.21        95.57       130.78        14.30 
TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YS 
       93.21        19.46        21.30        75.02        51.88        15.32 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       32.35        39.48         0.23         0.20        47.77        52.21 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        42.54        41.33        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       18.71        23.70        14.76        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 
       28.54        10.78        36.66        48.69         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      106.95       172.77         4.01        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
        2.96         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       16.24         9.40         0.10        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        0.10         0.46         2.50         5.56        13.78        29.59 
TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       34.19         0.23        26.04         0.13         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H 
        0.10         5.33        16.93        16.14        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        56.58        45.44 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
       41.49        68.32        69.27        35.44        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X 
       24.92        31.63        12.76        28.87        20.71        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         7.99         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W 
        9.44         5.88         7.96         7.59         0.23        10.42 
TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       13.25        10.95         9.01        13.61         9.60         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R 
       12.23        19.20         3.45         2.37         4.41        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23        13.41         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50        16.70        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y 
       12.99        88.83        94.03        32.65        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       25.81        29.85        32.61        35.15        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       123.65        75.25       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        26.47        18.61        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       36.13         7.92        26.93        23.51        19.99         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        20.68        15.06        18.54        28.37        27.16 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 
      169.84        10.39        99.06        30.05        31.59        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       30.44        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RJ 
       14.93        23.80        21.37        19.69         2.04        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       33.93        61.41        26.99        31.36        45.93        43.20 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        39.16        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                          0.23                           0.03 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                         21.53                          22.42 
[1] "0.2 - 156.2 (21.5)" "0.0 - 211.2 (22.4)"
[1] "hr=" "1.7"
D40V2, continuous
D40V3, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED    39  33
  DEL PEAK 20(11P15.1) WILD-TYPE 189 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED     39   33
  DEL PEAK 20(11P15.1) WILD-TYPE  189  251
        clus
vv       DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  FEMALE                           39                            189
  MALE                             33                            251
[1] 2 2
[1] FALSE
D40V4, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED    16  52
  DEL PEAK 20(11P15.1) WILD-TYPE 168 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED     16   52
  DEL PEAK 20(11P15.1) WILD-TYPE  168  243
     clus
vv    DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  NO                            16                            168
  YES                           52                            243
[1] 2 2
[1] FALSE
D40V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 20(11P15.1) MUTATED            43               15                14
  DEL PEAK 20(11P15.1) WILD-TYPE         151              114               175
D40V6, multiclass
                   clus
vv                  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  ASTROCYTOMA                                 43                            151
  OLIGOASTROCYTOMA                            15                            114
  OLIGODENDROGLIOMA                           14                            175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(11P15.1) MUTATED                                  0     0
  DEL PEAK 20(11P15.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.1) MUTATED                           2    70
  DEL PEAK 20(11P15.1) WILD-TYPE                        19   402
D40V7, multiclass
                                  clus
vv                                 DEL PEAK 20(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      70
                                  clus
vv                                 DEL PEAK 20(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED     4  66
  DEL PEAK 20(11P15.1) WILD-TYPE  28 380
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED      4   66
  DEL PEAK 20(11P15.1) WILD-TYPE   28  380
                        clus
vv                       DEL PEAK 20(11P15.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       DEL PEAK 20(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 28
  NOT HISPANIC OR LATINO                            380
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 21(12P13.1) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(12P13.1) MUTATED    22  15
  DEL PEAK 21(12P13.1) WILD-TYPE 361 110
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            37                            471 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            15                            110 
$`DEL PEAK 21(12P13.1) MUTATED`
TCGA-CS-6665 TCGA-CS-4943 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DU-5855 TCGA-DU-6403 
       51.55        36.36        44.52        31.63         6.81        11.64 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-A6S6 TCGA-DU-A76R 
        2.40        62.96        44.02        23.31        95.11        21.30 
TCGA-E1-5302 TCGA-E1-A7YI TCGA-E1-A7YS TCGA-E1-A7YV TCGA-FG-5965 TCGA-FG-6690 
       50.14         3.65        15.32        32.45        36.82        42.54 
TCGA-FG-A6J3 TCGA-FG-A711 TCGA-HT-7470 TCGA-HT-7879 TCGA-HT-8106 TCGA-HT-8108 
       22.26        48.69        40.11         3.68         0.10         2.50 
TCGA-HT-A5R7 TCGA-HW-A5KM TCGA-P5-A5EW TCGA-P5-A72X TCGA-S9-A6U1 TCGA-S9-A6UA 
       20.22        20.71         6.71        13.25        25.81         5.85 
TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A89V TCGA-TM-A84I 
       20.02        18.54        10.39        30.05        18.71        28.08 
TCGA-TQ-A7RF 
       21.37 

$`DEL PEAK 21(12P13.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       17.69        26.76        37.38        46.95        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.86        91.13        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L 
       30.21        39.78        37.45        33.57        72.95        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         8.45       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 
       46.06        65.75         1.22        87.45         7.04       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       154.36        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       94.32        18.94        25.91        60.30        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        33.27        29.85        31.69 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       24.43        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7T8 
       20.98        22.29        11.41        26.76        17.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI 
       84.33        51.52        37.38         7.50        44.42        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       78.21        95.57       130.78        14.30        29.13        93.21 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ 
       19.46        12.43        16.18        21.30        75.02        51.88 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z4 
        0.76        36.82       146.14        13.08        73.48       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        39.48         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       52.21        18.77        14.93        41.33        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       10.72        18.38        18.71        23.70        14.76        21.53 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87Q 
       15.02        16.44        28.54        10.78        36.66         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        11.54         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01        12.23         6.25         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        28.87        19.00        14.40        14.40         0.23 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        7.99         2.37         2.30         9.44         5.88         7.96 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 
        7.59         1.28         0.23        10.42        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        3.45         2.37         4.41        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23        13.41         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       88.83        94.03        32.65        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        41.10        40.93        35.38        36.82        24.39 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       29.85        32.61        35.15        98.24        95.93       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        26.47        18.61        18.64        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        26.93        23.51        19.99         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 
       20.68        15.06        28.37        27.16       169.84        99.06 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        20.48        54.77        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        65.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        23.80        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       40.41        44.09        36.69        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE 
       26.14        25.87        33.93        61.41        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       45.93        43.20        13.51         0.10         7.89        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       20.02        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                         95.11                         211.17 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                         21.37                          22.52 
[1] "0.1 - 95.1 (21.4)"  "0.0 - 211.2 (22.5)"
[1] "hr=" "2.3"
D41V2, continuous
D41V3, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED    17  21
  DEL PEAK 21(12P13.1) WILD-TYPE 211 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED     17   21
  DEL PEAK 21(12P13.1) WILD-TYPE  211  263
        clus
vv       DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  FEMALE                           17                            211
  MALE                             21                            263
[1] 2 2
[1] FALSE
D41V4, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED    13  23
  DEL PEAK 21(12P13.1) WILD-TYPE 171 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED     13   23
  DEL PEAK 21(12P13.1) WILD-TYPE  171  272
     clus
vv    DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  NO                            13                            171
  YES                           23                            272
[1] 2 2
[1] FALSE
D41V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 21(12P13.1) MUTATED            20                9                 9
  DEL PEAK 21(12P13.1) WILD-TYPE         174              120               180
D41V6, multiclass
                   clus
vv                  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  ASTROCYTOMA                                 20                            174
  OLIGOASTROCYTOMA                             9                            120
  OLIGODENDROGLIOMA                            9                            180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(12P13.1) MUTATED                                  0     0
  DEL PEAK 21(12P13.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(12P13.1) MUTATED                           1    36
  DEL PEAK 21(12P13.1) WILD-TYPE                        20   436
D41V7, multiclass
                                  clus
vv                                 DEL PEAK 21(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      36
                                  clus
vv                                 DEL PEAK 21(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       436
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED     0  35
  DEL PEAK 21(12P13.1) WILD-TYPE  32 411
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED      0   35
  DEL PEAK 21(12P13.1) WILD-TYPE   32  411
                        clus
vv                       DEL PEAK 21(12P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK 21(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            411
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 22(12Q12) MUTATION ANALYSIS
D42V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(12Q12) MUTATED    54  17
  DEL PEAK 22(12Q12) WILD-TYPE 329 108
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          71                          437 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          17                          108 
$`DEL PEAK 22(12Q12) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-DU-A76O TCGA-CS-4941 TCGA-DB-5275 TCGA-DB-5277 
       51.55        42.05        17.16         7.69        47.93        50.86 
TCGA-DB-5279 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A75K TCGA-DU-5871 TCGA-DU-6401 
       44.52        33.57        31.63        12.10        18.94        87.45 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-8166 TCGA-DU-8167 
        2.40        62.96       156.23        14.99        16.96        15.48 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76R TCGA-DU-A7TI TCGA-E1-5302 
       26.17        33.96        95.11        21.30        38.89        50.14 
TCGA-E1-5304 TCGA-E1-A7YH TCGA-E1-A7YK TCGA-E1-A7YS TCGA-E1-A7Z4 TCGA-FG-6689 
       41.13        93.21        12.43        15.32       145.05        14.93 
TCGA-FG-6690 TCGA-FG-A4MX TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7478 
       42.54        18.71        22.26        40.11         3.75         6.38 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8018 
       42.74        31.69         0.10        11.28        31.43        37.87 
TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8563 TCGA-HT-A5R7 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         2.50        28.27        20.22        16.83        17.52 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 
        6.71         2.30         7.59        10.42        13.25         9.01 
TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R3 
       18.77        25.81         5.85        14.07        18.54        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-TM-A84G TCGA-TM-A84I TCGA-TQ-A7RR 
       30.05        98.63        18.71        40.64        28.08        25.87 
TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85B 
       45.93         0.10        13.32        39.88        45.80 

$`DEL PEAK 22(12Q12) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-E1-A7YN TCGA-FG-8187 
       46.88        46.72        31.82        62.01        23.90        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 
       17.82        20.45        18.64        21.40        45.60        42.77 
TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
       59.38       117.50        43.89        36.36        60.10        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.26        21.01        53.62         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       37.38        46.95        48.30        49.94        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 
       81.96        75.25        72.92        91.13        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG 
       46.42        18.84        30.21        39.78        37.45        72.95 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M 
       27.81        29.23        14.40        18.51        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        23.21 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       17.46        13.71        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      154.36       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        33.27        29.85        31.69        24.43        24.99 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       25.55        21.57        20.98        22.29        11.41        26.76 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42         0.56        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI 
       78.21        95.57       130.78        14.30        29.13         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ TCGA-E1-A7YU 
       19.46        16.18        21.30        75.02        51.88         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 
       32.45        36.82       146.14        13.08        73.48        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       36.82        18.77        41.33        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.38        23.70        14.76        21.53        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 
       28.54        10.78        36.66        48.69         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67        11.54         0.13         0.03        16.54 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54        24.26        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 
        0.76        44.68         6.05         0.10        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 
        1.64        16.24         9.40        63.55         0.10        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
       12.23         6.25         0.46         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
        1.81        16.14        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       11.05         0.10        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       69.27        35.44        39.75        40.01        42.54        24.92 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X 
       31.63        12.76        28.87        20.71        19.00        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         0.23         7.99         2.37         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A733 
        7.96         1.28         0.23        11.64        10.95        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        4.41        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       32.65        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       35.38        36.82        24.39        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        36.13         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       20.02         8.19         2.04        20.68        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       27.16       169.84        10.39        31.59        20.48        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        65.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       15.98         2.04        40.41        44.09        36.69        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       31.20        30.05        26.14        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF 
       31.36        43.20        13.51         7.89        39.16        20.02 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        43.40        46.88        37.71        20.81 

  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                      156.23                       211.17 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                       22.26                        22.42 
[1] "0.1 - 156.2 (22.3)" "0.0 - 211.2 (22.4)"
[1] "hr=" "1.1"
D42V2, continuous
D42V3, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED    33  39
  DEL PEAK 22(12Q12) WILD-TYPE 195 245
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED     33   39
  DEL PEAK 22(12Q12) WILD-TYPE  195  245
        clus
vv       DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  FEMALE                         33                          195
  MALE                           39                          245
[1] 2 2
[1] FALSE
D42V4, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED    17  51
  DEL PEAK 22(12Q12) WILD-TYPE 167 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED     17   51
  DEL PEAK 22(12Q12) WILD-TYPE  167  244
     clus
vv    DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  NO                          17                          167
  YES                         51                          244
[1] 2 2
[1] FALSE
D42V5, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 22(12Q12) MUTATED            43               16                13
  DEL PEAK 22(12Q12) WILD-TYPE         151              113               176
D42V6, multiclass
                   clus
vv                  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  ASTROCYTOMA                               43                          151
  OLIGOASTROCYTOMA                          16                          113
  OLIGODENDROGLIOMA                         13                          176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(12Q12) MUTATED                                  0     0
  DEL PEAK 22(12Q12) WILD-TYPE                                1     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(12Q12) MUTATED                           1    69
  DEL PEAK 22(12Q12) WILD-TYPE                        20   403
D42V7, multiclass
                                  clus
vv                                 DEL PEAK 22(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    69
                                  clus
vv                                 DEL PEAK 22(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     403
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED     1  66
  DEL PEAK 22(12Q12) WILD-TYPE  31 380
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED      1   66
  DEL PEAK 22(12Q12) WILD-TYPE   31  380
                        clus
vv                       DEL PEAK 22(12Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         66
                        clus
vv                       DEL PEAK 22(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               31
  NOT HISPANIC OR LATINO                          380
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 23(13Q14.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(13Q14.2) MUTATED    94  49
  DEL PEAK 23(13Q14.2) WILD-TYPE 289  76
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           143                            365 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                            49                             76 
$`DEL PEAK 23(13Q14.2) MUTATED`
TCGA-CS-6670 TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-5275 TCGA-DB-5277 
       46.88        36.36        37.38        46.95        47.93        50.86 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 
       18.84        37.45        18.51        30.74        19.96        63.88 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 
       30.21        27.81        17.19        13.71        18.02         6.74 
TCGA-DU-5853 TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 
       13.38       211.17        65.75         1.22        94.52       114.08 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
       11.47       156.23        14.99        10.36         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-8168 
       44.02        25.91         5.10        19.13        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 
       33.27        31.69        26.17        33.96        21.57        20.98 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 
       21.30       139.04        84.33        38.89        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH 
       41.13        57.93       130.78        14.30        29.13        93.21 
TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 
       16.18        51.88        15.32        36.82       146.14        73.48 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6692 
       47.77        25.48        52.21        18.77        14.93        18.44 
TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       20.61        14.96        23.70        14.76        21.53        15.02 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 
       22.26        28.54        10.78         5.72        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 
        0.13        17.42         6.54        24.26       106.95       172.77 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7688 
      122.47         4.57        17.29        57.60         0.23        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7873 
       14.96         0.10         2.96        39.09         0.23        23.61 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 
       31.43         0.10        28.27        15.72        20.22         2.70 
TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X 
       16.14        17.52         0.10        41.49        68.32        14.40 
TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A737 TCGA-QH-A65S TCGA-QH-A65Z 
        2.30         7.59        10.42        12.23         2.53        14.04 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-RY-A847 
       14.53        13.61        13.41        16.73         9.90        30.67 
TCGA-S9-A6TV TCGA-S9-A6UA TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.77         5.85         7.92        26.93        23.51        19.99 
TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F 
       20.02        20.68        18.71        20.48        54.77        59.05 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RJ 
       28.08        40.83        18.61        14.93        15.98        40.41 
TCGA-TQ-A7RM TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-VM-A8CF TCGA-WY-A85E 
       36.69        26.99         7.89        20.02        20.81 

$`DEL PEAK 23(13Q14.2) WILD-TYPE`
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       51.55        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
       60.10        40.18         0.26        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       17.69        26.76        48.30        49.94        49.12       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       81.96        75.25        72.92        91.13        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       78.28        46.42        30.21        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66G TCGA-DH-A7UR 
       17.88        16.18        46.06        24.59        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 
       23.21        17.46        18.61        14.56        17.46         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        46.06        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 
       11.64       133.74        19.89        16.83         7.96         2.40 
TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       154.36       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-7304 
       90.77        30.67        26.30        94.32        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S6 
       16.96        29.85        24.43        24.99        25.55        95.11 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       22.29        11.41        26.76        17.98        51.52        37.38 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
        7.50        44.42         0.56        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YO 
       95.57         3.65        19.46        12.43        21.30        75.02 
TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 
        0.76        32.45        13.08       145.05        32.35        39.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
        0.23         0.20        36.82        42.54        41.33        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.09        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7467 
       18.71        16.44        36.66        48.69        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 
        6.67         0.03        16.54         3.75         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       75.19        95.93         4.01         5.03        29.85        23.18 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7676 
        3.16        22.06        45.99        56.09        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       29.59        34.19         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       27.35         0.10         5.33        16.93         1.81        16.83 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.65         2.43        10.52        15.35        11.05        56.58 
TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       45.44        69.27        35.44        39.75        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       24.92        31.63        12.76        28.87        20.71        19.00 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         7.99         2.37         9.44 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        5.88         7.96         1.28         0.23        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77W 
       10.95         9.01        13.61         9.60         7.56        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        3.45         2.37         4.41        15.16        12.62        15.85 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        14.83        12.23         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50        16.70        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX 
        2.07        19.59        62.17        87.12        41.10        40.93 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       35.38        36.82        24.39        25.81        29.85        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       35.15        98.24        95.93       123.65        75.25       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       85.55        38.56        84.99        31.10        19.86        26.47 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.61        18.64        14.07        36.13         8.19         2.04 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        18.54        28.37        27.16       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 
       99.06        30.05        98.63        31.59        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H 
       34.78        65.39        24.92        16.18        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF 
       24.16        24.79        33.24        25.38        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP 
       19.69         2.04        44.09        33.73        31.20        30.05 
TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 
       26.14        25.87        33.93        61.41        31.36        45.93 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       43.20        13.51         0.10        39.16        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        211.17                         182.33 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                         20.61                          23.47 
[1] "0.1 - 211.2 (20.6)" "0.0 - 182.3 (23.5)"
[1] "hr=" "1.5"
D43V2, continuous
D43V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED    58  86
  DEL PEAK 23(13Q14.2) WILD-TYPE 170 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     58   86
  DEL PEAK 23(13Q14.2) WILD-TYPE  170  198
        clus
vv       DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  FEMALE                           58                            170
  MALE                             86                            198
[1] 2 2
[1] FALSE
D43V4, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED    34 101
  DEL PEAK 23(13Q14.2) WILD-TYPE 150 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     34  101
  DEL PEAK 23(13Q14.2) WILD-TYPE  150  194
     clus
vv    DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  NO                            34                            150
  YES                          101                            194
[1] 2 2
[1] FALSE
D43V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 23(13Q14.2) MUTATED            64               37                43
  DEL PEAK 23(13Q14.2) WILD-TYPE         130               92               146
D43V6, multiclass
                   clus
vv                  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  ASTROCYTOMA                                 64                            130
  OLIGOASTROCYTOMA                            37                             92
  OLIGODENDROGLIOMA                           43                            146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(13Q14.2) MUTATED                                  1     1
  DEL PEAK 23(13Q14.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(13Q14.2) MUTATED                           9   132
  DEL PEAK 23(13Q14.2) WILD-TYPE                        12   340
D43V7, multiclass
                                  clus
vv                                 DEL PEAK 23(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                     132
                                  clus
vv                                 DEL PEAK 23(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED     7 130
  DEL PEAK 23(13Q14.2) WILD-TYPE  25 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED      7  130
  DEL PEAK 23(13Q14.2) WILD-TYPE   25  316
                        clus
vv                       DEL PEAK 23(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          130
                        clus
vv                       DEL PEAK 23(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            316
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 24(13Q34) MUTATION ANALYSIS
D44V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 24(13Q34) MUTATED    71  39
  DEL PEAK 24(13Q34) WILD-TYPE 312  86
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                         110                          398 
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                          39                           86 
$`DEL PEAK 24(13Q34) MUTATED`
TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DH-5140 TCGA-DH-A669 
       37.38        46.95        18.84        37.45        19.96        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5871 TCGA-DU-6392 
       27.81        17.19        13.71        18.02        18.94       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-8158 TCGA-DU-8165 
       14.99        10.36        18.94        44.02         5.10        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R 
       15.48        14.17        31.69        21.57        20.98        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD 
      139.04        84.33        67.46        41.13       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YW 
       29.13        93.21        16.18        51.88        15.32        36.82 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 
      146.14        13.08        47.77        25.48        52.21        14.93 
TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       18.44        20.61        14.96        14.76        21.53        15.02 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       22.26        10.78         5.72        11.54        40.11         0.13 
TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7611 TCGA-HT-7689 
       24.26       106.95         4.57        17.29        57.60        14.96 
TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7882 
        0.10         2.96         6.90        39.09         0.23         3.72 
TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A617 TCGA-HT-A61B TCGA-HW-7489 
       31.43         0.10        15.72        16.14        17.52        41.49 
TCGA-HW-7491 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W 
       68.32        19.00        14.40         2.30         7.59        10.42 
TCGA-P5-A737 TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 
       12.23        14.04        14.53        13.61        13.41        16.73 
TCGA-RY-A83Z TCGA-RY-A847 TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        9.90        30.67         5.85        26.93        23.51        20.02 
TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I 
       20.68        18.71        20.48        54.77        59.05        28.08 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RW TCGA-VM-A8CD 
       18.61        14.93        15.98        40.41        26.99         7.89 
TCGA-VM-A8CF TCGA-WY-A85E 
       20.02        20.81 

$`DEL PEAK 24(13Q34) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       43.89        36.36        60.10        40.18         0.26        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 
       53.62         6.38        17.69        26.76        48.30        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        91.13        44.52        36.56        78.28        46.42 
TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       30.21        39.78        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66G 
       30.74        16.18        63.88        46.06        24.59        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       54.25        23.21        17.46        18.61        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
        7.96         2.40        62.96       154.36       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        8.84       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       94.32        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP 
       23.74        14.60        20.68        21.40        16.96        33.27 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       29.85        24.43        26.17        24.99        33.96        25.55 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7TB 
       95.11        22.29        11.41        26.76        17.98        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         0.56        50.14 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YI 
       79.99        57.93       134.27        78.21        95.57         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YV 
       19.46        12.43        21.30        75.02         0.76        32.45 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 
       36.82        18.77        42.54        41.33        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.09        28.34        13.68        14.24        16.01 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FN-7833 
       23.70        16.44        28.54        36.66        48.69        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        0.10         6.67         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        6.54         6.38        40.34        75.19        95.93       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7607 
        4.01         5.03        29.85        23.18       122.47         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
       31.69         0.10        17.52        14.53        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        3.68         5.33        35.47        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.93         1.81        16.83        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 
       15.35        11.05         0.10        56.58        45.44        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       12.76        28.87        20.71        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
        7.99         2.37         9.44         5.88         7.96         1.28 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 
        9.60         7.56        19.20         3.45         2.37         4.41 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        19.33        14.83 
TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 
       12.23         9.17        10.29        14.53        16.34         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       32.65        30.87         5.46        28.08         2.07        19.59 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J1 
       18.64        14.07        36.13         7.92        19.99         8.19 
TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        15.06        18.54        28.37        27.16       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 
       10.39        99.06        30.05        98.63        31.59        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G 
       49.32        34.78        65.39        24.92        16.18        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RM 
       23.80        21.37        19.69         2.04        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU 
       33.73        31.20        30.05        26.14        25.87        33.93 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       61.41        31.36        45.93        43.20        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       39.16        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       51.06        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       46.88        37.71 

  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                      211.17                       182.33 
  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE 
                       18.97                        24.18 
[1] "0.1 - 211.2 (19.0)" "0.0 - 182.3 (24.2)"
[1] "hr=" "1.6"
D44V2, continuous
D44V3, binary
                              cls
clus                             0   1
  DEL PEAK 24(13Q34) MUTATED    45  65
  DEL PEAK 24(13Q34) WILD-TYPE 183 219
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(13Q34) MUTATED     45   65
  DEL PEAK 24(13Q34) WILD-TYPE  183  219
        clus
vv       DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE
  FEMALE                         45                          183
  MALE                           65                          219
[1] 2 2
[1] FALSE
D44V4, binary
                              cls
clus                             0   1
  DEL PEAK 24(13Q34) MUTATED    29  76
  DEL PEAK 24(13Q34) WILD-TYPE 155 219
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(13Q34) MUTATED     29   76
  DEL PEAK 24(13Q34) WILD-TYPE  155  219
     clus
vv    DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE
  NO                          29                          155
  YES                         76                          219
[1] 2 2
[1] FALSE
D44V5, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 24(13Q34) MUTATED            42               26                42
  DEL PEAK 24(13Q34) WILD-TYPE         152              103               147
D44V6, multiclass
                   clus
vv                  DEL PEAK 24(13Q34) MUTATED DEL PEAK 24(13Q34) WILD-TYPE
  ASTROCYTOMA                               42                          152
  OLIGOASTROCYTOMA                          26                          103
  OLIGODENDROGLIOMA                         42                          147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(13Q34) MUTATED                                  1     1
  DEL PEAK 24(13Q34) WILD-TYPE                                0     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(13Q34) MUTATED                           6   101
  DEL PEAK 24(13Q34) WILD-TYPE                        15   371
D44V7, multiclass
                                  clus
vv                                 DEL PEAK 24(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                   101
                                  clus
vv                                 DEL PEAK 24(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                              cls
clus                             0   1
  DEL PEAK 24(13Q34) MUTATED     6  98
  DEL PEAK 24(13Q34) WILD-TYPE  26 348
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(13Q34) MUTATED      6   98
  DEL PEAK 24(13Q34) WILD-TYPE   26  348
                        clus
vv                       DEL PEAK 24(13Q34) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         98
                        clus
vv                       DEL PEAK 24(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               26
  NOT HISPANIC OR LATINO                          348
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 25(14Q24.3) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(14Q24.3) MUTATED    76  45
  DEL PEAK 25(14Q24.3) WILD-TYPE 307  80
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                           121                            387 
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                            45                             80 
$`DEL PEAK 25(14Q24.3) MUTATED`
TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       21.40        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A64L TCGA-DB-A64O 
       60.10        49.94        44.52        18.84        24.20        25.48 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 
       19.96        63.88        46.06        18.02         6.74         6.81 
TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6403 TCGA-DU-6408 
       17.49        75.16        46.06        65.75        11.64       114.08 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7019 
        2.40        11.47        62.96        14.99         6.54        26.30 
TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
       10.36        18.94        60.30         5.10        23.74        19.13 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5304 TCGA-E1-5305 
       20.98        22.29        26.76        21.30        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YM 
       57.93        95.57       130.78        14.30        93.21        21.30 
TCGA-E1-A7YQ TCGA-E1-A7YS TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-EZ-7264 TCGA-FG-5963 
       51.88        15.32        32.45        13.08        39.48        25.48 
TCGA-FG-7643 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-HT-7477 
       20.09        32.61        38.27        23.70        22.26        24.26 
TCGA-HT-7603 TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7858 
       23.18        17.29         0.23        31.69        14.96        50.63 
TCGA-HT-7902 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A615 
       31.43        13.78        28.27        15.72         0.23        16.93 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61C TCGA-HW-7489 TCGA-HW-A5KK TCGA-P5-A5EV 
       16.14        16.83        17.65        41.49        12.76         0.23 
TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A77W TCGA-P5-A77X TCGA-QH-A6CS 
        7.99         2.30         7.96        19.20         3.45        19.33 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A870 TCGA-R8-A6MK 
       14.53        13.61         9.17        14.53        12.99        88.83 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WP 
        9.90        28.08        62.17        75.25        19.86        18.64 
TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R2 
       26.93        20.02         8.19        18.54        27.16        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84I TCGA-TM-A84Q 
       99.06        31.59        18.71        54.77        28.08        25.38 
TCGA-TQ-A7RF TCGA-TQ-A7RN TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8CB 
       21.37        33.73        25.87        26.99        31.36         0.10 
TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WY-A858 
        7.89        20.02        37.05        16.01        23.21        43.96 
TCGA-WY-A85B 
       45.80 

$`DEL PEAK 25(14Q24.3) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HW-7490 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       45.60        36.36        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        6.38        17.69        26.76        37.38        46.95        48.30 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       49.12       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       50.86        91.13        36.56        78.28        46.42        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P 
       39.78        37.45        33.57        72.95        31.63        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       24.59        30.21        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       23.21        17.46        13.71        18.61        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 
       13.38         8.45       182.33        18.94        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       52.11        22.42        49.02         1.22        87.45         7.04 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7008 
      133.74        19.89        16.83        94.52         7.96       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      154.36       105.21         8.84       117.40        90.77        30.67 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
        7.96        94.32        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        2.76        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        33.27        29.85        31.69        24.43        26.17 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
       24.99        33.96        25.55        21.57        95.11        11.41 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5311 
       44.42        38.89         0.56        50.14        67.46       134.27 
TCGA-E1-5318 TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       78.21        29.13         3.65        19.46        12.43        16.18 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 
       75.02         0.76        36.82       146.14        73.48       145.05 
TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       32.35         0.23         0.20        47.77        52.21        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        42.54        41.33        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        28.34        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       16.01        14.96        22.52        10.72        18.38        18.71 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        21.53        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       36.66        48.69         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
      106.95       172.77         4.01         5.03        29.85       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       42.74         0.10         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 
        6.25         0.10         0.46         2.50         5.56         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       29.59        34.19        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A61B 
       27.35         0.10         5.33         2.70         1.81        17.52 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        56.58 
TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       45.44        68.32        69.27        35.44        39.75        40.01 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       42.54        24.92        31.63        28.87        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40        14.40         6.71         2.37         9.44         5.88 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.59         1.28         0.23        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       10.95         9.01        13.61         9.60         7.56        12.23 
TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        2.37         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X5 
       14.04        14.83        12.23        13.41        10.29        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6ML 
       16.73         1.91        16.50        16.70        11.08        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       32.65        30.87         5.46         2.07        19.59        30.67 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        41.10        40.93        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       24.39        25.81        29.85        32.61        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       95.93         5.85       123.65       135.22        85.55        38.56 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       84.99        31.10        26.47        18.61        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.92        23.51        19.99         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C4 
       28.37       169.84        30.05        98.63        20.48        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        65.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        23.80        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       40.41        44.09        36.69        31.20        30.05        26.14 
TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
       33.93        61.41        45.93        43.20        13.51        39.16 
TCGA-VM-A8CH TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A 
       23.47         8.05        51.06        13.32        39.88        43.40 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE 
                         22.26                          22.52 
[1] "0.1 - 130.8 (22.3)" "0.0 - 211.2 (22.5)"
[1] "hr=" "2"  
D45V2, continuous
D45V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(14Q24.3) MUTATED    63  59
  DEL PEAK 25(14Q24.3) WILD-TYPE 165 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(14Q24.3) MUTATED     63   59
  DEL PEAK 25(14Q24.3) WILD-TYPE  165  225
        clus
vv       DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE
  FEMALE                           63                            165
  MALE                             59                            225
[1] 2 2
[1] FALSE
D45V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(14Q24.3) MUTATED    37  77
  DEL PEAK 25(14Q24.3) WILD-TYPE 147 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(14Q24.3) MUTATED     37   77
  DEL PEAK 25(14Q24.3) WILD-TYPE  147  218
     clus
vv    DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE
  NO                            37                            147
  YES                           77                            218
[1] 2 2
[1] FALSE
D45V5, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 25(14Q24.3) MUTATED            53               29                40
  DEL PEAK 25(14Q24.3) WILD-TYPE         141              100               149
D45V6, multiclass
                   clus
vv                  DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE
  ASTROCYTOMA                                 53                            141
  OLIGOASTROCYTOMA                            29                            100
  OLIGODENDROGLIOMA                           40                            149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(14Q24.3) MUTATED                                  1     3
  DEL PEAK 25(14Q24.3) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(14Q24.3) MUTATED                           6   108
  DEL PEAK 25(14Q24.3) WILD-TYPE                        15   364
D45V7, multiclass
                                  clus
vv                                 DEL PEAK 25(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                     108
                                  clus
vv                                 DEL PEAK 25(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(14Q24.3) MUTATED     7 104
  DEL PEAK 25(14Q24.3) WILD-TYPE  25 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(14Q24.3) MUTATED      7  104
  DEL PEAK 25(14Q24.3) WILD-TYPE   25  342
                        clus
vv                       DEL PEAK 25(14Q24.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 25(14Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            342
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 26(18Q23) MUTATION ANALYSIS
D46V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(18Q23) MUTATED    58  20
  DEL PEAK 26(18Q23) WILD-TYPE 325 105
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          78                          430 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                          20                          105 
$`DEL PEAK 26(18Q23) MUTATED`
TCGA-CS-6665 TCGA-DH-A66B TCGA-DU-7300 TCGA-CS-5396 TCGA-CS-6667 TCGA-DB-5275 
       51.55        42.05        62.01        53.62        48.30        47.93 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       44.52        36.56        39.78        72.95        31.63        24.20 
TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 
       19.96        63.88        30.21        17.46        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 
       17.46         8.45       182.33        52.11        94.52       154.36 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 
        6.54       117.40         5.10        24.43        17.98        57.93 
TCGA-E1-A7YM TCGA-E1-A7YS TCGA-FG-8185 TCGA-FG-8188 TCGA-HT-7476 TCGA-HT-7480 
       21.30        15.32        14.24        14.96         6.54        75.19 
TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-7873 
       17.29         0.23        31.69         2.96         0.23        23.61 
TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7489 
       34.19        15.72         0.10        16.14        11.05        41.49 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-P5-A5EX TCGA-P5-A72Z 
       68.32        40.01        31.63        20.71         7.99        11.64 
TCGA-QH-A65R TCGA-QH-A65Z TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX 
       15.16        14.04        28.08        62.17        41.10        40.93 
TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       75.25        38.56        31.10        19.86        26.47        18.64 
TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RF 
       28.37        10.39        40.64        28.08        24.16        21.37 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RW TCGA-VM-A8CA TCGA-WH-A86K TCGA-WY-A85B 
       15.98         2.04        26.99        13.51        13.32        45.80 

$`DEL PEAK 26(18Q23) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 
       46.88        46.72        31.82        17.16        23.90        20.09 
TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 
       17.82        20.45        18.64        21.40        45.60        42.77 
TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       59.38       117.50         7.69        43.89        36.36        60.10 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.26        21.01         6.38        17.69        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       37.38        46.95        49.94        49.12       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 TCGA-DB-A4X9 
       75.25        72.92        50.86        91.13        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64P 
       18.84        30.21        37.45        33.57        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       46.06        24.59        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 
       23.21        13.71        18.02         6.74        13.38         6.81 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16       211.17        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        16.83       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 
        2.40        11.47        62.96       156.23        14.99       105.21 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       31.69        26.17        24.99        33.96        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
       95.11        20.98        22.29        11.41        26.76        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      139.04        84.33        51.52        37.38         7.50        44.42 
TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       38.89         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE 
      134.27        78.21        95.57       130.78        14.30        29.13 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO 
       93.21         3.65        19.46        12.43        16.18        75.02 
TCGA-E1-A7YQ TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 
       51.88         0.76        32.45        36.82       146.14        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       73.48       145.05        32.35        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        52.21        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8189 
       20.61        20.09        28.34        13.68        16.01        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        21.53        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       10.78        36.66        48.69         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
        3.75        17.42        24.26         6.38        40.34        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
       13.78         0.23        29.59        28.27         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22         0.07        27.35         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.83        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 
       10.52        15.35         0.10        56.58        45.44        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KL 
       35.44        39.75        42.54        24.92        12.76        28.87 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       19.00        14.40        14.40         0.23         6.71         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         9.44         5.88         7.96         7.59         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        10.42        13.25        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
        4.41         2.53        12.62        15.85        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23        13.41         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50        16.70 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        5.46         9.90         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        35.38        36.82        24.39        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
      135.22        85.55        84.99        18.61        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        26.93        23.51        19.99        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        20.68        15.06        18.54        27.16       169.84 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        20.48 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       54.77        48.33        49.32        34.78        65.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       16.18        59.05        30.44        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RJ 
       25.38        18.61        14.93        23.80        19.69        40.41 
TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       44.09        36.69        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 
       25.87        33.93        61.41        31.36        45.93        43.20 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 
        0.10         7.89        39.16        20.02        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        46.88        37.71        20.81 

  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                      182.33                       211.17 
  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE 
                       25.45                        21.55 
[1] "0.1 - 182.3 (25.4)" "0.0 - 211.2 (21.6)"
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED    30  48
  DEL PEAK 26(18Q23) WILD-TYPE 198 236
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED     30   48
  DEL PEAK 26(18Q23) WILD-TYPE  198  236
        clus
vv       DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  FEMALE                         30                          198
  MALE                           48                          236
[1] 2 2
[1] FALSE
D46V4, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED    26  47
  DEL PEAK 26(18Q23) WILD-TYPE 158 248
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED     26   47
  DEL PEAK 26(18Q23) WILD-TYPE  158  248
     clus
vv    DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  NO                          26                          158
  YES                         47                          248
[1] 2 2
[1] FALSE
D46V5, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 26(18Q23) MUTATED            28               15                35
  DEL PEAK 26(18Q23) WILD-TYPE         166              114               154
D46V6, multiclass
                   clus
vv                  DEL PEAK 26(18Q23) MUTATED DEL PEAK 26(18Q23) WILD-TYPE
  ASTROCYTOMA                               28                          166
  OLIGOASTROCYTOMA                          15                          114
  OLIGODENDROGLIOMA                         35                          154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(18Q23) MUTATED                                  1     0
  DEL PEAK 26(18Q23) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(18Q23) MUTATED                           3    71
  DEL PEAK 26(18Q23) WILD-TYPE                        18   401
D46V7, multiclass
                                  clus
vv                                 DEL PEAK 26(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    71
                                  clus
vv                                 DEL PEAK 26(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     401
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                              cls
clus                             0   1
  DEL PEAK 26(18Q23) MUTATED     6  64
  DEL PEAK 26(18Q23) WILD-TYPE  26 382
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(18Q23) MUTATED      6   64
  DEL PEAK 26(18Q23) WILD-TYPE   26  382
                        clus
vv                       DEL PEAK 26(18Q23) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         64
                        clus
vv                       DEL PEAK 26(18Q23) WILD-TYPE
  HISPANIC OR LATINO                               26
  NOT HISPANIC OR LATINO                          382
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 27(19Q13.42) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(19Q13.42) MUTATED   220  54
  DEL PEAK 27(19Q13.42) WILD-TYPE 163  71
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                            274                             234 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                             54                              71 
$`DEL PEAK 27(19Q13.42) MUTATED`
TCGA-CS-6670 TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K 
       46.88        31.82        42.05        62.01        20.09        17.82 
TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4942 
       20.45        18.64        21.40        42.77        59.38        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 
       36.36        60.10         0.26        53.62        37.38        46.95 
TCGA-CS-6668 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 
       49.94       122.73        81.96        75.25        47.93        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH 
       91.13        44.52        18.84        30.21        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       24.20        30.12         5.98        31.40        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5144 
       14.40        12.10        11.24        19.96        63.88        24.59 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        23.21 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       14.56        17.46         6.81       182.33        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        75.16        46.06        65.75         1.22 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7010 
      114.08         7.96         2.40        62.96       154.36        14.99 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7302 
      117.40        90.77        30.67        94.32        18.94        60.30 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP 
       41.98         2.76        21.40        16.96        14.17        33.27 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R 
       31.69        25.55        21.57        95.11        22.29        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       17.98       139.04        84.33        51.52        37.38        44.42 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       50.14        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO TCGA-E1-A7YS 
      130.78        29.13        12.43        16.18        75.02        15.32 
TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z4 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 
        0.76       146.14       145.05        39.48         0.23        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       52.21        36.82        42.54        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A6IZ 
       20.61        16.01        14.96        38.27        18.71        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A711 TCGA-HT-7467 TCGA-HT-7468 
       16.44        22.26        36.66        48.69         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 
       11.54         0.13         0.03        17.42        75.19        95.93 
TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
      172.77         5.03         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 
       45.99        56.09         0.23        14.27        16.24        44.68 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
        0.10        31.69        14.96         2.96         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 
       39.09         0.23        37.15         0.33         0.13        35.47 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8563 
        1.64         9.40         6.25         5.56         0.23        28.27 
TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A618 
       15.72        26.04        20.22         0.07        16.93        16.83 
TCGA-HT-A61B TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       17.52        15.35        11.05         0.10        56.58        45.44 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X 
       68.32        35.44        40.01        24.92        31.63        14.40 
TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F6 
        0.23         7.99         2.30         9.44         7.96         1.28 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W 
       11.64        10.95         9.01         9.60        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        3.45         2.37         4.41        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        14.83        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.73         1.91        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A845 
       32.65        30.87         5.46         9.90        28.08        19.59 
TCGA-RY-A847 TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       30.67        18.77        41.10        40.93        35.38        36.82 
TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       24.39        29.85        32.61       123.65        75.25       135.22 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ 
       38.56        84.99        31.10        26.47        18.64        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.92        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C5 
       28.37        27.16       169.84        31.59        18.71        49.32 
TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.92        40.64        24.16        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH 
       18.61        14.93        23.80        21.37        19.69        15.98 
TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU 
        2.04        36.69        33.73        31.20        26.14        33.93 
TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       26.99        31.36        45.93        13.51         0.10        39.16 
TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A858 
       37.05        23.21        51.06        43.96 

$`DEL PEAK 27(19Q13.42) WILD-TYPE`
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DU-A76O TCGA-E1-A7YN TCGA-HW-7490 TCGA-CS-4938 
       51.55        46.72        17.16        23.90        45.60       117.50 
TCGA-CS-4941 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        7.69        40.18        21.01         6.38        17.69        26.76 
TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       48.30        49.12        72.92        36.56        78.28        46.42 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X 
       39.78        37.45        33.57        25.48        27.45        18.51 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A7UT TCGA-DH-A7UU 
       17.88        30.74        16.18        46.06        17.46        13.71 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 
       18.61        18.02         6.74        13.38         8.45        18.94 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
      211.17        49.02        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7011 
       19.89        16.83        94.52        11.47       156.23       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7299 
        6.54         8.84        26.30        10.36         7.96        44.02 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       25.91        23.31         5.10        23.74        14.60        20.68 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       19.13        15.48        29.85        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TI 
       33.96        20.98        11.41        26.76         7.50        38.89 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5307 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YI 
        0.56        67.46        57.93        14.30        93.21         3.65 
TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z2 
       19.46        21.30        51.88        32.45        36.82        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6689 
       73.48        32.35         0.20        25.48        18.77        14.93 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       41.33        18.44        20.09        28.34        13.68        14.24 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A60J 
       22.52        32.61        10.72        18.38        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7470 
       21.53        28.54        10.78         5.72        27.52        40.11 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75         6.54        24.26         6.38        40.34 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7611 
      106.95         4.01        29.85        23.18       122.47        57.60 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 
        0.16         0.76         6.05        42.74         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       17.52        39.48        19.23        50.63         0.49        23.61 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 
        3.68         5.33         3.72        11.28        31.43        16.24 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        37.87        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS 
        0.46         2.50        13.78        29.59        34.19         0.23 
TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 
        0.13        27.35         0.10         5.33         2.70         1.81 
TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HW-7489 TCGA-HW-7493 
       16.14        17.65         2.43        10.52        41.49        69.27 
TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       39.75        42.54        12.76        28.87        20.71        19.00 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A72U 
       14.40         6.71         2.37         5.88         7.59         0.23 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-P5-A736 TCGA-QH-A65S TCGA-QH-A6CS 
       10.42        13.25        13.61         7.56         2.53        19.33 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        13.61        12.23        10.29        16.50        16.70 
TCGA-RY-A843 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 
        2.07        62.17        87.12        25.81        35.15        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ 
       95.93         5.85        85.55        19.86        18.61        14.07 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 
       26.93        19.99        20.02        18.54        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       30.05        98.63        20.48        54.77        48.33        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L 
       65.39        16.18        59.05        30.44        28.08        40.83 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-VM-A8C9 
       40.41        44.09        30.05        25.87        61.41        43.20 
TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K 
        7.89        20.02        23.47        16.01         8.05        13.32 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                         182.33                          211.17 
  DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE 
                          24.18                           20.58 
[1] "0.0 - 182.3 (24.2)" "0.1 - 211.2 (20.6)"
[1] "hr=" "1.9"
D47V2, continuous
D47V3, binary
                                 cls
clus                                0   1
  DEL PEAK 27(19Q13.42) MUTATED   126 152
  DEL PEAK 27(19Q13.42) WILD-TYPE 102 132
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED    126  152
  DEL PEAK 27(19Q13.42) WILD-TYPE  102  132
        clus
vv       DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE
  FEMALE                           126                             102
  MALE                             152                             132
[1] 2 2
[1] FALSE
D47V4, binary
                                 cls
clus                                0   1
  DEL PEAK 27(19Q13.42) MUTATED   119 143
  DEL PEAK 27(19Q13.42) WILD-TYPE  65 152
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED    119  143
  DEL PEAK 27(19Q13.42) WILD-TYPE   65  152
     clus
vv    DEL PEAK 27(19Q13.42) MUTATED DEL PEAK 27(19Q13.42) WILD-TYPE
  NO                            119                              65
  YES                           143                             152
[1] 2 2
[1] FALSE
D47V5, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 27(19Q13.42) MUTATED            60               64
  DEL PEAK 27(19Q13.42) WILD-TYPE         134               65
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 27(19Q13.42) MUTATED                 154
  DEL PEAK 27(19Q13.42) WILD-TYPE                35
D47V6, multiclass
                   clus
vv                  DEL PEAK 27(19Q13.42) MUTATED
  ASTROCYTOMA                                  60
  OLIGOASTROCYTOMA                             64
  OLIGODENDROGLIOMA                           154
                   clus
vv                  DEL PEAK 27(19Q13.42) WILD-TYPE
  ASTROCYTOMA                                   134
  OLIGOASTROCYTOMA                               65
  OLIGODENDROGLIOMA                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(19Q13.42) MUTATED                                  0     6
  DEL PEAK 27(19Q13.42) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(19Q13.42) MUTATED                          10   255
  DEL PEAK 27(19Q13.42) WILD-TYPE                        11   217
D47V7, multiclass
                                  clus
vv                                 DEL PEAK 27(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      255
                                  clus
vv                                 DEL PEAK 27(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     11
  WHITE                                                        217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                                 cls
clus                                0   1
  DEL PEAK 27(19Q13.42) MUTATED    18 244
  DEL PEAK 27(19Q13.42) WILD-TYPE  14 202
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.42) MUTATED     18  244
  DEL PEAK 27(19Q13.42) WILD-TYPE   14  202
                        clus
vv                       DEL PEAK 27(19Q13.42) MUTATED
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           244
                        clus
vv                       DEL PEAK 27(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                  14
  NOT HISPANIC OR LATINO                             202
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 28(22Q13.31) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(22Q13.31) MUTATED    42  35
  DEL PEAK 28(22Q13.31) WILD-TYPE 341  90
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             77                             431 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                             35                              90 
$`DEL PEAK 28(22Q13.31) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6186 TCGA-DB-5273 TCGA-DB-5277 
       36.36        40.18         6.38        17.69        81.96        50.86 
TCGA-DB-A4XB TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A75O TCGA-DH-A669 TCGA-DU-5847 
       30.21        24.20        25.48        30.74        30.21        18.02 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-7007 
        6.74        13.38        65.75         7.04       133.74        62.96 
TCGA-DU-7008 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
      156.23        10.36        18.94        41.98         5.10        23.74 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       19.13        15.48        33.27        24.43        26.17        33.96 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YE 
       11.41        26.76        67.46        41.13       130.78        29.13 
TCGA-E1-A7YJ TCGA-E1-A7YM TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7Z2 TCGA-FG-7643 
       19.46        21.30        15.32         0.76        13.08        20.09 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7477 TCGA-HT-7611 TCGA-HT-7686 TCGA-HT-7688 
       23.70        21.53        24.26        57.60        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         0.49         2.70        16.14        16.83        17.52 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A780 TCGA-QH-A6CS 
        2.43        12.76         1.28         0.23         2.37        19.33 
TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7R2 
        9.90        62.17         5.85        26.93        20.02        10.39 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84G TCGA-TQ-A7RM 
       98.63        18.71        20.48        24.92        40.64        36.69 
TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-VM-A8CF TCGA-WH-A86K TCGA-WY-A859 
       26.99         7.89        20.02        13.32        39.88 

$`DEL PEAK 28(22Q13.31) WILD-TYPE`
TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 
       51.55        46.88        46.72        31.82        42.05        62.01 
TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       17.16        23.90        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 
       21.40        45.60        42.77        59.38       117.50         7.69 
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6188 
       43.89        60.10         0.26        21.01        53.62        26.76 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       37.38        46.95        48.30        49.94        49.12       122.73 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        46.42        18.84        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        31.63        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       17.88        16.18        19.96        63.88        46.06        24.59 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        23.21        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 
       13.71        18.61        14.56        17.46         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        75.16        46.06         1.22        87.45 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
        2.40        11.47       154.36        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        8.84       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       94.32        44.02        25.91        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TR 
       14.60        20.68        21.40        16.96        14.17        29.85 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       31.69        24.99        25.55        21.57        95.11        20.98 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       22.29        21.30        17.98       139.04        84.33        51.52 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       37.38         7.50        44.42        38.89         0.56        50.14 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD 
       79.99        57.93       134.27        78.21        95.57        14.30 
TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YO TCGA-E1-A7YQ 
       93.21         3.65        12.43        16.18        75.02        51.88 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-E1-A7Z6 
       32.45        36.82       146.14        73.48       145.05        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       39.48         0.23         0.20        47.77        25.48        52.21 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        42.54        41.33        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       10.72        18.38        18.71        14.76        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       22.26        28.54        10.78        36.66        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        56.09         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       16.93         1.81        17.65        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.44        39.75        40.01        42.54        24.92        31.63 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       28.87        20.71        19.00        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         7.99         2.37         2.30         9.44         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        7.96         7.59        10.42        13.25        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W 
        9.01        13.61         9.60         7.56        12.23        19.20 
TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        3.45         4.41        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        14.83        14.53        13.61        12.23        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50        16.70        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       32.65        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        41.10        40.93        35.38 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       36.82        24.39        25.81        29.85        32.61        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       123.65        75.25       135.22        85.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       38.56        84.99        31.10        19.86        26.47        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.64        14.07        36.13         7.92        23.51        19.99 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        20.68        15.06        18.54        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C3 
       27.16       169.84        99.06        30.05        31.59        54.77 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        65.39        16.18        59.05 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RG 
       25.38        18.61        14.93        23.80        21.37        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO 
       15.98         2.04        40.41        44.09        33.73        31.20 
TCGA-TQ-A7RP TCGA-TQ-A7RQ TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE 
       30.05        26.14        25.87        33.93        61.41        31.36 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       45.93        43.20        13.51         0.10        39.16        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                         156.23                          211.17 
  DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE 
                          21.30                           22.52 
[1] "0.1 - 156.2 (21.3)" "0.0 - 211.2 (22.5)"
[1] "hr=" "2.4"
D48V2, continuous
D48V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(22Q13.31) MUTATED    32  45
  DEL PEAK 28(22Q13.31) WILD-TYPE 196 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED     32   45
  DEL PEAK 28(22Q13.31) WILD-TYPE  196  239
        clus
vv       DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE
  FEMALE                            32                             196
  MALE                              45                             239
[1] 2 2
[1] FALSE
D48V4, binary
                                 cls
clus                                0   1
  DEL PEAK 28(22Q13.31) MUTATED    17  52
  DEL PEAK 28(22Q13.31) WILD-TYPE 167 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED     17   52
  DEL PEAK 28(22Q13.31) WILD-TYPE  167  243
     clus
vv    DEL PEAK 28(22Q13.31) MUTATED DEL PEAK 28(22Q13.31) WILD-TYPE
  NO                             17                             167
  YES                            52                             243
[1] 2 2
[1] FALSE
D48V5, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 28(22Q13.31) MUTATED            44               15
  DEL PEAK 28(22Q13.31) WILD-TYPE         150              114
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 28(22Q13.31) MUTATED                  18
  DEL PEAK 28(22Q13.31) WILD-TYPE               171
D48V6, multiclass
                   clus
vv                  DEL PEAK 28(22Q13.31) MUTATED
  ASTROCYTOMA                                  44
  OLIGOASTROCYTOMA                             15
  OLIGODENDROGLIOMA                            18
                   clus
vv                  DEL PEAK 28(22Q13.31) WILD-TYPE
  ASTROCYTOMA                                   150
  OLIGOASTROCYTOMA                              114
  OLIGODENDROGLIOMA                             171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(22Q13.31) MUTATED                                  1     0
  DEL PEAK 28(22Q13.31) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(22Q13.31) MUTATED                           2    74
  DEL PEAK 28(22Q13.31) WILD-TYPE                        19   398
D48V7, multiclass
                                  clus
vv                                 DEL PEAK 28(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       74
                                  clus
vv                                 DEL PEAK 28(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     19
  WHITE                                                        398
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(22Q13.31) MUTATED     3  67
  DEL PEAK 28(22Q13.31) WILD-TYPE  29 379
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(22Q13.31) MUTATED      3   67
  DEL PEAK 28(22Q13.31) WILD-TYPE   29  379
                        clus
vv                       DEL PEAK 28(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            67
                        clus
vv                       DEL PEAK 28(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  29
  NOT HISPANIC OR LATINO                             379
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 29(XQ21.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 29(XQ21.1) MUTATED    52  25
  DEL PEAK 29(XQ21.1) WILD-TYPE 331 100
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           77                           431 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                           25                           100 
$`DEL PEAK 29(XQ21.1) MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF 
       51.55        48.30        47.93        50.86        44.52        33.57 
TCGA-DB-A4XH TCGA-DB-A64W TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-6404 TCGA-DU-6410 
       31.63        14.40        19.96        18.02       133.74         7.96 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8158 
       11.47       156.23        14.99        30.67        94.32         5.10 
TCGA-DU-8168 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5311 
       14.17        22.29        21.30        17.98        50.14       134.27 
TCGA-E1-A7YE TCGA-E1-A7YK TCGA-E1-A7YS TCGA-E1-A7YV TCGA-E1-A7Z4 TCGA-EZ-7264 
       29.13        12.43        15.32        32.45       145.05        39.48 
TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7471 
        0.23        52.21        15.02        22.26        11.54         0.13 
TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-A61B TCGA-HW-7491 
        0.23        31.69         0.10         2.96        17.52        68.32 
TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72Z 
       42.54        19.00        14.40         7.96         1.28        11.64 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A65Z TCGA-QH-A6CX TCGA-QH-A6X4 
       12.23        19.20         2.37        14.04        12.23        14.53 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6WP 
       16.73         1.91         9.90        87.12        18.77        18.64 
TCGA-S9-A7IS TCGA-S9-A7QW TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84I 
        7.92        15.06        20.48        49.32        65.39        28.08 
TCGA-TQ-A7RF TCGA-TQ-A7RM TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       21.37        36.69        61.41        26.99        31.36        45.93 
TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VV-A829 TCGA-WH-A86K TCGA-WY-A859 
        7.89        20.02        37.05        13.32        39.88 

$`DEL PEAK 29(XQ21.1) WILD-TYPE`
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-DU-7300 TCGA-DU-A76O 
       46.88        46.72        31.82        42.05        62.01        17.16 
TCGA-E1-A7YN TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-A619 
       23.90        20.09        17.82        20.45        18.64        21.40 
TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       45.60        42.77        59.38       117.50         7.69        43.89 
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       36.36        60.10        40.18         0.26        21.01        53.62 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 
        6.38        17.69        26.76        37.38        46.95        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
       49.12       122.73        81.96        75.25        72.92        91.13 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       36.56        78.28        46.42        18.84        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       37.45        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5142 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        63.88        46.06 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       24.59        30.21        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       23.21        17.46        13.71        18.61        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
       11.64        19.89        16.83        94.52       114.08         2.40 
TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       154.36       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 
       90.77        26.30        10.36         7.96        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       33.27        29.85        31.69        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
       33.96        25.55        21.57        95.11        20.98        11.41 
TCGA-DU-A76L TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76       139.04        84.33        51.52        37.38         7.50 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42        38.89         0.56        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YH 
       57.93        78.21        95.57       130.78        14.30        93.21 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YQ 
        3.65        19.46        16.18        21.30        75.02        51.88 
TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-E1-A7Z6 
        0.76        36.82       146.14        13.08        73.48        32.35 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        47.77        25.48        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       42.54        41.33        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        28.34        13.68        14.24        16.01 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A70Y 
       18.71        23.70        14.76        21.53        16.44        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       10.78        36.66        48.69         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        6.67        40.11         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 
       44.68         6.05        42.74         0.10        14.96         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
        1.81        16.14        16.83        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        56.58        45.44        41.49 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       69.27        35.44        39.75        40.01        24.92        31.63 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       12.76        28.87        20.71        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 
        7.99         2.37         2.30         9.44         5.88         7.59 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.23        10.42        13.25        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65S 
        9.60         7.56         3.45         4.41        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        15.85        19.33        14.83        14.53        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6XA TCGA-QH-A6XC 
       13.41         9.17        10.29        16.34        16.50        16.70 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       11.08        12.99        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        5.46        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       41.10        40.93        35.38        36.82        24.39        25.81 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       29.85        32.61        35.15        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      123.65        75.25       135.22        85.55        38.56        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        19.86        26.47        18.61        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       26.93        23.51        19.99        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       20.68        18.54        28.37        27.16       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 
       99.06        30.05        98.63        31.59        18.71        54.77 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       48.33        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI 
       18.61        14.93        23.80        19.69        15.98         2.04 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RP TCGA-TQ-A7RQ 
       40.41        44.09        33.73        31.20        30.05        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       25.87        33.93        43.20        13.51         0.10        39.16 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       23.47        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE 
                        19.96                         23.31 
[1] "0.1 - 156.2 (20.0)" "0.0 - 211.2 (23.3)"
[1] "hr=" "1.4"
D49V2, continuous
D49V3, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED    38  40
  DEL PEAK 29(XQ21.1) WILD-TYPE 190 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED     38   40
  DEL PEAK 29(XQ21.1) WILD-TYPE  190  244
        clus
vv       DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  FEMALE                          38                           190
  MALE                            40                           244
[1] 2 2
[1] FALSE
D49V4, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED    22  51
  DEL PEAK 29(XQ21.1) WILD-TYPE 162 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED     22   51
  DEL PEAK 29(XQ21.1) WILD-TYPE  162  244
     clus
vv    DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  NO                           22                           162
  YES                          51                           244
[1] 2 2
[1] FALSE
D49V5, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 29(XQ21.1) MUTATED            31               16                31
  DEL PEAK 29(XQ21.1) WILD-TYPE         163              113               158
D49V6, multiclass
                   clus
vv                  DEL PEAK 29(XQ21.1) MUTATED DEL PEAK 29(XQ21.1) WILD-TYPE
  ASTROCYTOMA                                31                           163
  OLIGOASTROCYTOMA                           16                           113
  OLIGODENDROGLIOMA                          31                           158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(XQ21.1) MUTATED                                  0     1
  DEL PEAK 29(XQ21.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(XQ21.1) MUTATED                           1    75
  DEL PEAK 29(XQ21.1) WILD-TYPE                        20   397
D49V7, multiclass
                                  clus
vv                                 DEL PEAK 29(XQ21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     75
                                  clus
vv                                 DEL PEAK 29(XQ21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 29(XQ21.1) MUTATED     5  67
  DEL PEAK 29(XQ21.1) WILD-TYPE  27 379
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 29(XQ21.1) MUTATED      5   67
  DEL PEAK 29(XQ21.1) WILD-TYPE   27  379
                        clus
vv                       DEL PEAK 29(XQ21.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK 29(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                27
  NOT HISPANIC OR LATINO                           379
[1] 2 2
[1] FALSE
